diff --git a/sequence_processing_pipeline/Commands.py b/sequence_processing_pipeline/Commands.py
index 2879cb03..d8e2e166 100644
--- a/sequence_processing_pipeline/Commands.py
+++ b/sequence_processing_pipeline/Commands.py
@@ -14,7 +14,6 @@ def split_similar_size_bins(data_location_path, max_file_list_size_in_gb,
     :param batch_prefix: Path + file-name prefix for output-files.
     :return: The number of output-files created, size of largest bin.
     '''
-
     # to prevent issues w/filenames like the ones below from being mistaken
     # for R1 or R2 files, use determine_orientation().
     # LS_8_22_2014_R2_SRE_S2_L007_I1_001.fastq.gz
@@ -22,7 +21,6 @@ def split_similar_size_bins(data_location_path, max_file_list_size_in_gb,
 
     # since the names of all fastq files are being scanned for orientation,
     # collect all of them instead of mistakenly pre-filtering some files.
-    # fastq_paths = glob.glob(data_location_path + '/*/*_R?_*.fastq.gz')
     fastq_paths = glob.glob(data_location_path + '/*/*.fastq.gz')
     fastq_paths = [x for x in fastq_paths
                    if determine_orientation(x) in ['R1', 'R2']]
diff --git a/sequence_processing_pipeline/tests/data/SeqCounts.csv b/sequence_processing_pipeline/tests/data/SeqCounts.csv
index 18e905ab..fe601c4c 100644
--- a/sequence_processing_pipeline/tests/data/SeqCounts.csv
+++ b/sequence_processing_pipeline/tests/data/SeqCounts.csv
@@ -1,3 +1,3 @@
 Sample_ID,raw_reads_r1r2,Lane
-LS_8_22_2014_R1_SRE,140798056,1
-LS_8_22_2014_R2_SRE,128928324,1
+Test_8_22_2014_R1_example,140798056,4
+Test_8_22_2014_R2_example,128928324,4
diff --git a/sequence_processing_pipeline/tests/data/seq_counts_logs/seq_count_2679966_1.err b/sequence_processing_pipeline/tests/data/seq_counts_logs/seq_count_2679966_1.err
index 8ef9a94c..a1c9e65c 100644
--- a/sequence_processing_pipeline/tests/data/seq_counts_logs/seq_count_2679966_1.err
+++ b/sequence_processing_pipeline/tests/data/seq_counts_logs/seq_count_2679966_1.err
@@ -1,3 +1,3 @@
 This is an example .err file produced by seq_counts.sbatch.
 Additional details removed.
-+ seqtk size REMOVED/working_dir/8edbdee2-da52-4278-af40-267185bbcd7e/TRIntegrateJob/integrated/LS_8_22_2014_R2_SRE_S2_L007_R1_001.fastq.gz
++ seqtk size REMOVED/working_dir/8edbdee2-da52-4278-af40-267185bbcd7e/TRIntegrateJob/integrated/Test_8_22_2014_R2_example_S2_L007_R1_001.fastq.gz
diff --git a/sequence_processing_pipeline/tests/data/seq_counts_logs/seq_count_2679966_1.out b/sequence_processing_pipeline/tests/data/seq_counts_logs/seq_count_2679966_1.out
index 06753505..94552607 100644
--- a/sequence_processing_pipeline/tests/data/seq_counts_logs/seq_count_2679966_1.out
+++ b/sequence_processing_pipeline/tests/data/seq_counts_logs/seq_count_2679966_1.out
@@ -1,2 +1,2 @@
-REMOVED/8edbdee2-da52-4278-af40-267185bbcd7e/TRIntegrateJob/integrated/LS_8_22_2014_R2_SRE_S2_L007_R1_001.fastq.gz
+REMOVED/8edbdee2-da52-4278-af40-267185bbcd7e/TRIntegrateJob/integrated/Test_8_22_2014_R2_example_S2_L007_R1_001.fastq.gz
 64464162	8345327641
diff --git a/sequence_processing_pipeline/tests/data/seq_counts_logs/seq_count_2679966_2.err b/sequence_processing_pipeline/tests/data/seq_counts_logs/seq_count_2679966_2.err
index ab1c2b3e..5de27ab2 100644
--- a/sequence_processing_pipeline/tests/data/seq_counts_logs/seq_count_2679966_2.err
+++ b/sequence_processing_pipeline/tests/data/seq_counts_logs/seq_count_2679966_2.err
@@ -1,3 +1,3 @@
 This is an example .err file produced by seq_counts.sbatch.
 Additional details removed.
-+ seqtk size REMOVED/working_dir/8edbdee2-da52-4278-af40-267185bbcd7e/TRIntegrateJob/integrated/LS_8_22_2014_R1_SRE_S3_L007_R1_001.fastq.gz
\ No newline at end of file
++ seqtk size REMOVED/working_dir/8edbdee2-da52-4278-af40-267185bbcd7e/TRIntegrateJob/integrated/Test_8_22_2014_R1_example_S3_L007_R1_001.fastq.gz
diff --git a/sequence_processing_pipeline/tests/data/seq_counts_logs/seq_count_2679966_2.out b/sequence_processing_pipeline/tests/data/seq_counts_logs/seq_count_2679966_2.out
index 439eac51..7e3bf3a4 100644
--- a/sequence_processing_pipeline/tests/data/seq_counts_logs/seq_count_2679966_2.out
+++ b/sequence_processing_pipeline/tests/data/seq_counts_logs/seq_count_2679966_2.out
@@ -1,2 +1,2 @@
-REMOVED/8edbdee2-da52-4278-af40-267185bbcd7e/TRIntegrateJob/integrated/LS_8_22_2014_R1_SRE_S3_L007_R1_001.fastq.gz
+REMOVED/8edbdee2-da52-4278-af40-267185bbcd7e/TRIntegrateJob/integrated/Test_8_22_2014_R1_example_S3_L007_R1_001.fastq.gz
 70399028	9293296513
diff --git a/sequence_processing_pipeline/tests/data/seq_counts_logs/seq_count_2679966_4.err b/sequence_processing_pipeline/tests/data/seq_counts_logs/seq_count_2679966_4.err
index 4c635b60..dce819a0 100644
--- a/sequence_processing_pipeline/tests/data/seq_counts_logs/seq_count_2679966_4.err
+++ b/sequence_processing_pipeline/tests/data/seq_counts_logs/seq_count_2679966_4.err
@@ -1,3 +1,3 @@
 This is an example .err file produced by seq_counts.sbatch.
 Additional details removed.
-+ seqtk size REMOVED/working_dir/8edbdee2-da52-4278-af40-267185bbcd7e/TRIntegrateJob/integrated/LS_8_22_2014_R1_SRE_S3_L007_R2_001.fastq.gz
++ seqtk size REMOVED/working_dir/8edbdee2-da52-4278-af40-267185bbcd7e/TRIntegrateJob/integrated/Test_8_22_2014_R1_example_S3_L007_R2_001.fastq.gz
diff --git a/sequence_processing_pipeline/tests/data/seq_counts_logs/seq_count_2679966_4.out b/sequence_processing_pipeline/tests/data/seq_counts_logs/seq_count_2679966_4.out
index da6697a7..1973f6f5 100644
--- a/sequence_processing_pipeline/tests/data/seq_counts_logs/seq_count_2679966_4.out
+++ b/sequence_processing_pipeline/tests/data/seq_counts_logs/seq_count_2679966_4.out
@@ -1,2 +1,2 @@
-REMOVED/8edbdee2-da52-4278-af40-267185bbcd7e/TRIntegrateJob/integrated/LS_8_22_2014_R1_SRE_S3_L007_R2_001.fastq.gz
+REMOVED/8edbdee2-da52-4278-af40-267185bbcd7e/TRIntegrateJob/integrated/Test_8_22_2014_R1_example_S3_L007_R2_001.fastq.gz
 70399028	9317943166
diff --git a/sequence_processing_pipeline/tests/data/seq_counts_logs/seq_count_2679966_5.err b/sequence_processing_pipeline/tests/data/seq_counts_logs/seq_count_2679966_5.err
index 360f379f..2bf591a4 100644
--- a/sequence_processing_pipeline/tests/data/seq_counts_logs/seq_count_2679966_5.err
+++ b/sequence_processing_pipeline/tests/data/seq_counts_logs/seq_count_2679966_5.err
@@ -1,3 +1,3 @@
 This is an example .err file produced by seq_counts.sbatch.
 Additional details removed.
-+ seqtk size REMOVED/working_dir/8edbdee2-da52-4278-af40-267185bbcd7e/TRIntegrateJob/integrated/LS_8_22_2014_R2_SRE_S2_L007_I1_001.fastq.gz
++ seqtk size REMOVED/working_dir/8edbdee2-da52-4278-af40-267185bbcd7e/TRIntegrateJob/integrated/Test_8_22_2014_R2_example_S2_L007_I1_001.fastq.gz
diff --git a/sequence_processing_pipeline/tests/data/seq_counts_logs/seq_count_2679966_5.out b/sequence_processing_pipeline/tests/data/seq_counts_logs/seq_count_2679966_5.out
index ba88f823..19d4b351 100644
--- a/sequence_processing_pipeline/tests/data/seq_counts_logs/seq_count_2679966_5.out
+++ b/sequence_processing_pipeline/tests/data/seq_counts_logs/seq_count_2679966_5.out
@@ -1,2 +1,2 @@
-REMOVED/8edbdee2-da52-4278-af40-267185bbcd7e/TRIntegrateJob/integrated/LS_8_22_2014_R2_SRE_S2_L007_I1_001.fastq.gz
+REMOVED/8edbdee2-da52-4278-af40-267185bbcd7e/TRIntegrateJob/integrated/Test_8_22_2014_R2_example_S2_L007_I1_001.fastq.gz
 70399028	1267182504
diff --git a/sequence_processing_pipeline/tests/data/seq_counts_logs/seq_count_2679966_6.err b/sequence_processing_pipeline/tests/data/seq_counts_logs/seq_count_2679966_6.err
index b28a1701..b587244d 100644
--- a/sequence_processing_pipeline/tests/data/seq_counts_logs/seq_count_2679966_6.err
+++ b/sequence_processing_pipeline/tests/data/seq_counts_logs/seq_count_2679966_6.err
@@ -1,3 +1,3 @@
 This is an example .err file produced by seq_counts.sbatch.
 Additional details removed.
-+ seqtk size REMOVED/working_dir/8edbdee2-da52-4278-af40-267185bbcd7e/TRIntegrateJob/integrated/LS_8_22_2014_R2_SRE_S2_L007_R2_001.fastq.gz
++ seqtk size REMOVED/working_dir/8edbdee2-da52-4278-af40-267185bbcd7e/TRIntegrateJob/integrated/Test_8_22_2014_R2_example_S2_L007_R2_001.fastq.gz
diff --git a/sequence_processing_pipeline/tests/data/seq_counts_logs/seq_count_2679966_6.out b/sequence_processing_pipeline/tests/data/seq_counts_logs/seq_count_2679966_6.out
index 67ff467e..813c7a6c 100644
--- a/sequence_processing_pipeline/tests/data/seq_counts_logs/seq_count_2679966_6.out
+++ b/sequence_processing_pipeline/tests/data/seq_counts_logs/seq_count_2679966_6.out
@@ -1,2 +1,2 @@
-REMOVED/8edbdee2-da52-4278-af40-267185bbcd7e/TRIntegrateJob/integrated/LS_8_22_2014_R2_SRE_S2_L007_R2_001.fastq.gz
+REMOVED/8edbdee2-da52-4278-af40-267185bbcd7e/TRIntegrateJob/integrated/Test_8_22_2014_R2_example_S2_L007_R2_001.fastq.gz
 64464162	8370238082
diff --git a/sequence_processing_pipeline/tests/data/seq_counts_logs/seq_count_2679966_7.err b/sequence_processing_pipeline/tests/data/seq_counts_logs/seq_count_2679966_7.err
index 069c0ac9..e353b3f4 100644
--- a/sequence_processing_pipeline/tests/data/seq_counts_logs/seq_count_2679966_7.err
+++ b/sequence_processing_pipeline/tests/data/seq_counts_logs/seq_count_2679966_7.err
@@ -1,3 +1,3 @@
 This is an example .err file produced by seq_counts.sbatch.
 Additional details removed.
-+ seqtk size REMOVED/working_dir/8edbdee2-da52-4278-af40-267185bbcd7e/TRIntegrateJob/integrated/LS_8_22_2014_R1_SRE_S3_L007_I1_001.fastq.gz
\ No newline at end of file
++ seqtk size REMOVED/working_dir/8edbdee2-da52-4278-af40-267185bbcd7e/TRIntegrateJob/integrated/Test_8_22_2014_R1_example_S3_L007_I1_001.fastq.gz
diff --git a/sequence_processing_pipeline/tests/data/seq_counts_logs/seq_count_2679966_7.out b/sequence_processing_pipeline/tests/data/seq_counts_logs/seq_count_2679966_7.out
index 75b103ce..33df5d01 100644
--- a/sequence_processing_pipeline/tests/data/seq_counts_logs/seq_count_2679966_7.out
+++ b/sequence_processing_pipeline/tests/data/seq_counts_logs/seq_count_2679966_7.out
@@ -1,2 +1,2 @@
-REMOVED/8edbdee2-da52-4278-af40-267185bbcd7e/TRIntegrateJob/integrated/LS_8_22_2014_R1_SRE_S3_L007_I1_001.fastq.gz
+REMOVED/8edbdee2-da52-4278-af40-267185bbcd7e/TRIntegrateJob/integrated/Test_8_22_2014_R1_example_S3_L007_I1_001.fastq.gz
 64464162	1160354916
diff --git a/sequence_processing_pipeline/tests/data/tellseq_metag_dummy_sample_sheet.csv b/sequence_processing_pipeline/tests/data/tellseq_metag_dummy_sample_sheet.csv
index 105330fd..dccf189d 100644
--- a/sequence_processing_pipeline/tests/data/tellseq_metag_dummy_sample_sheet.csv
+++ b/sequence_processing_pipeline/tests/data/tellseq_metag_dummy_sample_sheet.csv
@@ -1,135 +1,136 @@
-[Header],,,,,,,,
-IEMFileVersion,1,,,,,,,
-SheetType,tellseq_metag,,,,,,,
-SheetVersion,10,,,,,,,
-Investigator Name,Knight,,,,,,,
-Experiment Name,RKL0151,,,,,,,
-Date,5/6/24,,,,,,,
-Workflow,GenerateFASTQ,,,,,,,
-Application,FASTQ Only,,,,,,,
-Assay,Metagenomic,,,,,,,
-Description,,,,,,,,
-Chemistry,Default,,,,,,,
-,,,,,,,,
-[Reads],,,,,,,,
-151,,,,,,,,
-151,,,,,,,,
-,,,,,,,,
-[Settings],,,,,,,,
-ReverseComplement,0,,,,,,,
-,,,,,,,,
-[Data],,,,,,,,
-Sample_ID,Sample_Name,Sample_Plate,well_id_384,barcode_id,Sample_Project,Well_description,Lane,
-LS_8_10_2013_SRE,LS.8.10.2013.SRE,LS_Donor_SS_Samples_P1,A1,C501,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.8.10.2013.SRE,1,
-LS_12_17_2014_SRE,LS.12.17.2014.SRE,LS_Donor_SS_Samples_P1,B1,C509,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.12.17.2014.SRE,1,
-LS_4_4_2015_SRE,LS.4.4.2015.SRE,LS_Donor_SS_Samples_P1,C1,C502,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.4.4.2015.SRE,1,
-LS_2_23_2015_SRE,LS.2.23.2015.SRE,LS_Donor_SS_Samples_P1,D1,C510,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.2.23.2015.SRE,1,
-LS_9_28_2014_SRE,LS.9.28.2014.SRE,LS_Donor_SS_Samples_P1,E1,C503,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.9.28.2014.SRE,1,
-LS_12_14_2013_SRE,LS.12.14.2013.SRE,LS_Donor_SS_Samples_P1,F1,C511,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.12.14.2013.SRE,1,
-LS_4_7_2013_SRE,LS.4.7.2013.SRE,LS_Donor_SS_Samples_P1,G1,C504,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.4.7.2013.SRE,1,
-LS_7_14_2013_SRE,LS.7.14.2013.SRE,LS_Donor_SS_Samples_P1,H1,C512,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.7.14.2013.SRE,1,
-LS_10_27_2013_SRE,LS.10.27.2013.SRE,LS_Donor_SS_Samples_P1,I1,C505,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.10.27.2013.SRE,1,
-LS_1_19_2014_SRE,LS.1.19.2014.SRE,LS_Donor_SS_Samples_P1,J1,C513,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.1.19.2014.SRE,1,
-LS_9_3_2013_SRE,LS.9.3.2013.SRE,LS_Donor_SS_Samples_P1,K1,C506,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.9.3.2013.SRE,1,
-LS_2_25_2013_SRE,LS.2.25.2013.SRE,LS_Donor_SS_Samples_P1,L1,C514,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.2.25.2013.SRE,1,
-LS_7_26_2015_SRE,LS.7.26.2015.SRE,LS_Donor_SS_Samples_P1,M1,C507,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.7.26.2015.SRE,1,
-LS_2_17_2014_SRE,LS.2.17.2014.SRE,LS_Donor_SS_Samples_P1,N1,C515,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.2.17.2014.SRE,1,
-LS_6_29_2015_SRE,LS.6.29.2015.SRE,LS_Donor_SS_Samples_P1,O1,C508,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.6.29.2015.SRE,1,
-LS_3_24_2015_SRE,LS.3.24.2015.SRE,LS_Donor_SS_Samples_P1,P1,C516,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.3.24.2015.SRE,1,
-LS_1_6_2015_SRE,LS.1.6.2015.SRE,LS_Donor_SS_Samples_P1,A2,C517,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.1.6.2015.SRE,1,
-T_LS_7_15_15B_SRE,T.LS.7.15.15B.SRE,LS_Donor_SS_Samples_P1,B2,C525,Tellseq_Shortread_Metagenomic_Analysis_10283,T.LS.7.15.15B.SRE,1,
-LS_6_9_2013_SRE,LS.6.9.2013.SRE,LS_Donor_SS_Samples_P1,C2,C518,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.6.9.2013.SRE,1,
-Person A_SRE,Person A.SRE,LS_Donor_SS_Samples_P1,D2,C526,Tellseq_Shortread_Metagenomic_Analysis_10283,Person A.SRE,1,
-LS_8_22_2014_R2_SRE,LS.8.22.2014.R2.SRE,LS_Donor_SS_Samples_P1,E2,C519,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.8.22.2014.R2.SRE,1,
-Person B_SRE,Person B.SRE,LS_Donor_SS_Samples_P1,F2,C527,Tellseq_Shortread_Metagenomic_Analysis_10283,Person B.SRE,1,
-LS_8_22_2014_R1_SRE,LS.8.22.2014.R1.SRE,LS_Donor_SS_Samples_P1,G2,C520,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.8.22.2014.R1.SRE,1,
-Person C_SRE,Person C.SRE,LS_Donor_SS_Samples_P1,H2,C528,Tellseq_Shortread_Metagenomic_Analysis_10283,Person C.SRE,1,
-LS_12_28_2011_SRE,LS.12.28.2011.SRE,LS_Donor_SS_Samples_P1,I2,C521,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.12.28.2011.SRE,1,
-Person D_SRE,Person D.SRE,LS_Donor_SS_Samples_P1,J2,C529,Tellseq_Shortread_Metagenomic_Analysis_10283,Person D.SRE,1,
-LS_5_4_2014_SRE,LS.5.4.2014.SRE,LS_Donor_SS_Samples_P1,K2,C522,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.5.4.2014.SRE,1,
-45208_1_1,45208.1.1,UROBIOME_TEST_MF_SAMPLES_P2,L2,C530,Tellseq_Shortread_Metagenomic_Analysis_10283,45208.1.1,1,
-LS_11_6_2012_SRE,LS.11.6.2012.SRE,LS_Donor_SS_Samples_P1,M2,C523,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.11.6.2012.SRE,1,
-45248_2_2,45248.2.2,UROBIOME_TEST_MF_SAMPLES_P2,N2,C531,Tellseq_Shortread_Metagenomic_Analysis_10283,45248.2.2,1,
-LS_4_3_2012_SRE,LS.4.3.2012.SRE,LS_Donor_SS_Samples_P1,O2,C524,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.4.3.2012.SRE,1,
-45261_2_1,45261.2.1,UROBIOME_TEST_MF_SAMPLES_P2,P2,C532,Tellseq_Shortread_Metagenomic_Analysis_10283,45261.2.1,1,
-45272_11_2,45272.11.2,UROBIOME_TEST_MF_SAMPLES_P2,A3,C533,Tellseq_Shortread_Metagenomic_Analysis_10283,45272.11.2,1,
-T_LS_7_12_15A,T.LS.7.12.15A,Larry_Smarr_Plus_Donor_Samples_P3,B3,C541,Tellseq_Shortread_Metagenomic_Analysis_10283,T.LS.7.12.15A,1,
-45316_8_1,45316.8.1,UROBIOME_TEST_MF_SAMPLES_P2,C3,C534,Tellseq_Shortread_Metagenomic_Analysis_10283,45316.8.1,1,
-T_LS_7_8_15A,T.LS.7.8.15A,Larry_Smarr_Plus_Donor_Samples_P3,D3,C542,Tellseq_Shortread_Metagenomic_Analysis_10283,T.LS.7.8.15A,1,
-45327_7_2,45327.7.2,UROBIOME_TEST_MF_SAMPLES_P2,E3,C535,Tellseq_Shortread_Metagenomic_Analysis_10283,45327.7.2,1,
-LS_8_10_2013,LS.8.10.2013,LS_Time_Series_ABSQ_P4,F3,C543,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.8.10.2013,1,
-45272_1_swab_2,45272.1.swab.2,UROBIOME_TEST_MF_SAMPLES_P2,G3,C536,Tellseq_Shortread_Metagenomic_Analysis_10283,45272.1.swab.2,1,
-LS_6_29_2015,LS.6.29.2015,LS_Time_Series_ABSQ_P4,H3,C544,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.6.29.2015,1,
-45326_1_swab_2,45326.1.swab.2,UROBIOME_TEST_MF_SAMPLES_P2,I3,C537,Tellseq_Shortread_Metagenomic_Analysis_10283,45326.1.swab.2,1,
-LS_3_8_2015,LS.3.8.2015,LS_Time_Series_ABSQ_P4,J3,C545,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.3.8.2015,1,
-T_LS_7_19_15A,T.LS.7.19.15A,Larry_Smarr_Plus_Donor_Samples_P3,K3,C538,Tellseq_Shortread_Metagenomic_Analysis_10283,T.LS.7.19.15A,1,
-LS_4_29_2013,LS.4.29.2013,LS_Time_Series_ABSQ_P4,L3,C546,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.4.29.2013,1,
-T_LS_7_15_15B,T.LS.7.15.15B,Larry_Smarr_Plus_Donor_Samples_P3,M3,C539,Tellseq_Shortread_Metagenomic_Analysis_10283,T.LS.7.15.15B,1,
-LS_11_16_2014,LS.11.16.2014,LS_Time_Series_ABSQ_P4,N3,C547,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.11.16.2014,1,
-T_LS_7_19_15B,T.LS.7.19.15B,Larry_Smarr_Plus_Donor_Samples_P3,O3,C540,Tellseq_Shortread_Metagenomic_Analysis_10283,T.LS.7.19.15B,1,
-LS_1_19_2014,LS.1.19.2014,LS_Time_Series_ABSQ_P4,P3,C548,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.1.19.2014,1,
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-LS_1_14_2015,LS.1.14.2015,LS_Time_Series_ABSQ_P4,G4,C552,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.1.14.2015,1,
-Marine_Sediment_10_12cm_R2,Marine.Sediment.10.12cm.R2,MarineSediment_Donor_LarrySmarr_NoProK_P5,H4,C560,Tellseq_Shortread_Metagenomic_Analysis_10283,Marine.Sediment.10.12cm.R2,1,
-LS_8_25_2014,LS.8.25.2014,LS_Time_Series_ABSQ_P4,I4,C553,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.8.25.2014,1,
-Marine_Sediment_15_17cm_R1,Marine.Sediment.15.17cm.R1,MarineSediment_Donor_LarrySmarr_NoProK_P5,J4,C561,Tellseq_Shortread_Metagenomic_Analysis_10283,Marine.Sediment.15.17cm.R1,1,
-LS_1_26_2013,LS.1.26.2013,LS_Time_Series_ABSQ_P4,K4,C554,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.1.26.2013,1,
-Marine_Sediment_20_22cm_R1,Marine.Sediment.20.22cm.R1,MarineSediment_Donor_LarrySmarr_NoProK_P5,L4,C562,Tellseq_Shortread_Metagenomic_Analysis_10283,Marine.Sediment.20.22cm.R1,1,
-LS_6_16_2014,LS.6.16.2014,LS_Time_Series_ABSQ_P4,M4,C555,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.6.16.2014,1,
-Marine_Sediment_25_27cm_R2,Marine.Sediment.25.27cm.R2,MarineSediment_Donor_LarrySmarr_NoProK_P5,N4,C563,Tellseq_Shortread_Metagenomic_Analysis_10283,Marine.Sediment.25.27cm.R2,1,
-LS_7_27_2014,LS.7.27.2014,LS_Time_Series_ABSQ_P4,O4,C556,Tellseq_Shortread_Metagenomic_Analysis_10283,LS.7.27.2014,1,
-Marine_Sediment_30_32cm_R3,Marine.Sediment.30.32cm.R3,MarineSediment_Donor_LarrySmarr_NoProK_P5,P4,C564,Tellseq_Shortread_Metagenomic_Analysis_10283,Marine.Sediment.30.32cm.R3,1,
-Person_A_R3,Person.A.R3,MarineSediment_Donor_LarrySmarr_NoProK_P5,A5,C565,Tellseq_Shortread_Metagenomic_Analysis_10283,Person.A.R3,1,
-Soil_SynCom_T4_2_Tube5,Soil.SynCom.T4.2.Tube5,16_member_community_native_soil_P6,B5,C573,Tellseq_Shortread_Metagenomic_Analysis_10283,Soil.SynCom.T4.2.Tube5,1,
-Person_B_R2,Person.B.R2,MarineSediment_Donor_LarrySmarr_NoProK_P5,C5,C566,Tellseq_Shortread_Metagenomic_Analysis_10283,Person.B.R2,1,
-A21,A21,Tumor_Community_P7,D5,C574,Tellseq_Shortread_Metagenomic_Analysis_10283,A21,1,
-Person_C_R4,Person.C.R4,MarineSediment_Donor_LarrySmarr_NoProK_P5,E5,C567,Tellseq_Shortread_Metagenomic_Analysis_10283,Person.C.R4,1,
-A23,A23,Tumor_Community_P7,F5,C575,Tellseq_Shortread_Metagenomic_Analysis_10283,A23,1,
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-A27,A27,Tumor_Community_P7,H5,C576,Tellseq_Shortread_Metagenomic_Analysis_10283,A27,1,
-Soil_SynCom_T1_2_Tube1,Soil.SynCom.T1.2.Tube1,16_member_community_native_soil_P6,I5,C569,Tellseq_Shortread_Metagenomic_Analysis_10283,Soil.SynCom.T1.2.Tube1,1,
-A30,A30,Tumor_Community_P7,J5,C577,Tellseq_Shortread_Metagenomic_Analysis_10283,A30,1,
-Soil _SynCom_T2_2_Tube2,Soil .SynCom.T2.2.Tube2,16_member_community_native_soil_P6,K5,C570,Tellseq_Shortread_Metagenomic_Analysis_10283,Soil .SynCom.T2.2.Tube2,1,
-A31,A31,Tumor_Community_P7,L5,C578,Tellseq_Shortread_Metagenomic_Analysis_10283,A31,1,
-Soil_SynCom_T3_2_Tube3,Soil.SynCom.T3.2.Tube3,16_member_community_native_soil_P6,M5,C571,Tellseq_Shortread_Metagenomic_Analysis_10283,Soil.SynCom.T3.2.Tube3,1,
-S1_T1_A,S1.T1.A,Tumor_Community_P7,N5,C579,Tellseq_Shortread_Metagenomic_Analysis_10283,S1.T1.A,1,
-Soil_SynCom_T4_1_Tube4,Soil.SynCom.T4.1.Tube4,16_member_community_native_soil_P6,O5,C572,Tellseq_Shortread_Metagenomic_Analysis_10283,Soil.SynCom.T4.1.Tube4,1,
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-S1_T1_1CIM_A,S1.T1.1CIM.A,Tumor_Community_P7,B6,C589,Tellseq_Shortread_Metagenomic_Analysis_10283,S1.T1.1CIM.A,1,
-S2_MT1_1HBI_Y_A,S2.MT1.1HBI.Y.A,Tumor_Community_P7,C6,C582,Tellseq_Shortread_Metagenomic_Analysis_10283,S2.MT1.1HBI.Y.A,1,
-S1_M1_B_1CIM_A,S1.M1.B.1CIM.A,Tumor_Community_P7,D6,C590,Tellseq_Shortread_Metagenomic_Analysis_10283,S1.M1.B.1CIM.A,1,
-S1_T1_B_LBM_A,S1.T1.B.LBM.A,Tumor_Community_P7,E6,C583,Tellseq_Shortread_Metagenomic_Analysis_10283,S1.T1.B.LBM.A,1,
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-BLANK_M15_cancer_patient,BLANK.M15.cancer.patient,Tumor_Community_P7,H6,C592,Tellseq_Shortread_Metagenomic_Analysis_10283,BLANK.M15.cancer.patient,1,
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-,,,,,,,,
-[Bioinformatics],,,,,,,,
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-Tellseq_Shortread_Metagenomic_Analysis_10283,10283,TRUE,GATCGGAAGAGCACACGTCTGAACTCCAGTCAC,GATCGGAAGAGCGTCGTGTAGGGAAAGGAGTGT,TRUE,tellseq,tellseq metagenomics,FALSE
-,,,,,,,,
-[Contact],,,,,,,,
-Sample_Project,Email,,,,,,,
-Tellseq_Shortread_Metagenomic_Analysis_10283,cbrenchy@gmail.com,,,,,,,
-,,,,,,,,
-[SampleContext],,,,,,,,
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\ No newline at end of file
+[Header],,,,,,,,
+IEMFileVersion,1,,,,,,,
+SheetType,tellseq_metag,,,,,,,
+SheetVersion,10,,,,,,,
+Investigator Name,Knight,,,,,,,
+Experiment Name,RKLtest,,,,,,,
+Date,5/6/24,,,,,,,
+Workflow,GenerateFASTQ,,,,,,,
+Application,FASTQ Only,,,,,,,
+Assay,Metagenomic,,,,,,,
+Description,,,,,,,,
+Chemistry,Default,,,,,,,
+,,,,,,,,
+[Reads],,,,,,,,
+151,,,,,,,,
+151,,,,,,,,
+,,,,,,,,
+[Settings],,,,,,,,
+ReverseComplement,0,,,,,,,
+,,,,,,,,
+[Data],,,,,,,,
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+Test_12_17_2014_example,Test.12.17.2014.example,Test_Donor_SS_Samples_P1,B1,C509,Tellseq_Shortread_Metagenomic_Analysis_00000,Test.12.17.2014.example,4,
+Test_4_4_2015_example,Test.4.4.2015.example,Test_Donor_SS_Samples_P1,C1,C502,Tellseq_Shortread_Metagenomic_Analysis_00000,Test.4.4.2015.example,4,
+Test_2_23_2015_example,Test.2.23.2015.example,Test_Donor_SS_Samples_P1,D1,C510,Tellseq_Shortread_Metagenomic_Analysis_00000,Test.2.23.2015.example,4,
+Test_9_28_2014_example,Test.9.28.2014.example,Test_Donor_SS_Samples_P1,E1,C503,Tellseq_Shortread_Metagenomic_Analysis_00000,Test.9.28.2014.example,4,
+Test_12_14_2013_example,Test.12.14.2013.example,Test_Donor_SS_Samples_P1,F1,C511,Tellseq_Shortread_Metagenomic_Analysis_00000,Test.12.14.2013.example,4,
+Test_4_7_2013_example,Test.4.7.2013.example,Test_Donor_SS_Samples_P1,G1,C504,Tellseq_Shortread_Metagenomic_Analysis_00000,Test.4.7.2013.example,4,
+Test_7_14_2013_example,Test.7.14.2013.example,Test_Donor_SS_Samples_P1,H1,C512,Tellseq_Shortread_Metagenomic_Analysis_00000,Test.7.14.2013.example,4,
+Test_10_27_2013_example,Test.10.27.2013.example,Test_Donor_SS_Samples_P1,I1,C505,Tellseq_Shortread_Metagenomic_Analysis_00000,Test.10.27.2013.example,4,
+Test_1_19_2014_example,Test.1.19.2014.example,Test_Donor_SS_Samples_P1,J1,C513,Tellseq_Shortread_Metagenomic_Analysis_00000,Test.1.19.2014.example,4,
+Test_9_3_2013_example,Test.9.3.2013.example,Test_Donor_SS_Samples_P1,K1,C506,Tellseq_Shortread_Metagenomic_Analysis_00000,Test.9.3.2013.example,4,
+Test_2_25_2013_example,Test.2.25.2013.example,Test_Donor_SS_Samples_P1,L1,C514,Tellseq_Shortread_Metagenomic_Analysis_00000,Test.2.25.2013.example,4,
+Test_7_26_2015_example,Test.7.26.2015.example,Test_Donor_SS_Samples_P1,M1,C507,Tellseq_Shortread_Metagenomic_Analysis_00000,Test.7.26.2015.example,4,
+Test_2_17_2014_example,Test.2.17.2014.example,Test_Donor_SS_Samples_P1,N1,C515,Tellseq_Shortread_Metagenomic_Analysis_00000,Test.2.17.2014.example,4,
+Test_6_29_2015_example,Test.6.29.2015.example,Test_Donor_SS_Samples_P1,O1,C508,Tellseq_Shortread_Metagenomic_Analysis_00000,Test.6.29.2015.example,4,
+Test_3_24_2015_example,Test.3.24.2015.example,Test_Donor_SS_Samples_P1,P1,C516,Tellseq_Shortread_Metagenomic_Analysis_00000,Test.3.24.2015.example,4,
+Test_1_6_2015_example,Test.1.6.2015.example,Test_Donor_SS_Samples_P1,A2,C517,Tellseq_Shortread_Metagenomic_Analysis_00000,Test.1.6.2015.example,4,
+T_Test_7_15_15B_example,T.Test.7.15.15B.example,Test_Donor_SS_Samples_P1,B2,C525,Tellseq_Shortread_Metagenomic_Analysis_00000,T.Test.7.15.15B.example,4,
+Test_6_9_2013_example,Test.6.9.2013.example,Test_Donor_SS_Samples_P1,C2,C518,Tellseq_Shortread_Metagenomic_Analysis_00000,Test.6.9.2013.example,4,
+example_A_example,example.A.example,Test_Donor_SS_Samples_P1,D2,C526,Tellseq_Shortread_Metagenomic_Analysis_00000,example.A.example,4,
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+example_B_example,example.B.example,Test_Donor_SS_Samples_P1,F2,C527,Tellseq_Shortread_Metagenomic_Analysis_00000,example.B.example,4,
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+45261_2_1,45261.2.1,UROBIOME_TEST_MF_SAMPLES_P2,P2,C532,Tellseq_Shortread_Metagenomic_Analysis_00000,45261.2.1,4,
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+45272_1_swab_2,45272.1.swab.2,UROBIOME_TEST_MF_SAMPLES_P2,G3,C536,Tellseq_Shortread_Metagenomic_Analysis_00000,45272.1.swab.2,4,
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+T_Test_7_19_15A,T.Test.7.19.15A,Example_Plus_Donor_Samples_P3,K3,C538,Tellseq_Shortread_Metagenomic_Analysis_00000,T.Test.7.19.15A,4,
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+T_Test_7_15_15B,T.Test.7.15.15B,Example_Plus_Donor_Samples_P3,M3,C539,Tellseq_Shortread_Metagenomic_Analysis_00000,T.Test.7.15.15B,4,
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+T_Test_7_19_15B,T.Test.7.19.15B,Example_Plus_Donor_Samples_P3,O3,C540,Tellseq_Shortread_Metagenomic_Analysis_00000,T.Test.7.19.15B,4,
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+Test_11_10_2013,Test.11.10.2013,Test_Time_Series_ABSQ_P4,C4,C550,Tellseq_Shortread_Metagenomic_Analysis_00000,Test.11.10.2013,4,
+Marine_Sediment_0_2cm_R1,Marine.Sediment.0.2cm.R1,MarineSediment_Donor_Test_NoProK_P5,D4,C558,Tellseq_Shortread_Metagenomic_Analysis_00000,Marine.Sediment.0.2cm.R1,4,
+Test_3_23_2014,Test.3.23.2014,Test_Time_Series_ABSQ_P4,E4,C551,Tellseq_Shortread_Metagenomic_Analysis_00000,Test.3.23.2014,4,
+Marine_Sediment_5_7cm_R1,Marine.Sediment.5.7cm.R1,MarineSediment_Donor_Test_NoProK_P5,F4,C559,Tellseq_Shortread_Metagenomic_Analysis_00000,Marine.Sediment.5.7cm.R1,4,
+Test_1_14_2015,Test.1.14.2015,Test_Time_Series_ABSQ_P4,G4,C552,Tellseq_Shortread_Metagenomic_Analysis_00000,Test.1.14.2015,4,
+Marine_Sediment_10_12cm_R2,Marine.Sediment.10.12cm.R2,MarineSediment_Donor_Test_NoProK_P5,H4,C560,Tellseq_Shortread_Metagenomic_Analysis_00000,Marine.Sediment.10.12cm.R2,4,
+Test_8_25_2014,Test.8.25.2014,Test_Time_Series_ABSQ_P4,I4,C553,Tellseq_Shortread_Metagenomic_Analysis_00000,Test.8.25.2014,4,
+Marine_Sediment_15_17cm_R1,Marine.Sediment.15.17cm.R1,MarineSediment_Donor_Test_NoProK_P5,J4,C561,Tellseq_Shortread_Metagenomic_Analysis_00000,Marine.Sediment.15.17cm.R1,4,
+Test_1_26_2013,Test.1.26.2013,Test_Time_Series_ABSQ_P4,K4,C554,Tellseq_Shortread_Metagenomic_Analysis_00000,Test.1.26.2013,4,
+Marine_Sediment_20_22cm_R1,Marine.Sediment.20.22cm.R1,MarineSediment_Donor_Test_NoProK_P5,L4,C562,Tellseq_Shortread_Metagenomic_Analysis_00000,Marine.Sediment.20.22cm.R1,4,
+Test_6_16_2014,Test.6.16.2014,Test_Time_Series_ABSQ_P4,M4,C555,Tellseq_Shortread_Metagenomic_Analysis_00000,Test.6.16.2014,4,
+Marine_Sediment_25_27cm_R2,Marine.Sediment.25.27cm.R2,MarineSediment_Donor_Test_NoProK_P5,N4,C563,Tellseq_Shortread_Metagenomic_Analysis_00000,Marine.Sediment.25.27cm.R2,4,
+Test_7_27_2014,Test.7.27.2014,Test_Time_Series_ABSQ_P4,O4,C556,Tellseq_Shortread_Metagenomic_Analysis_00000,Test.7.27.2014,4,
+Marine_Sediment_30_32cm_R3,Marine.Sediment.30.32cm.R3,MarineSediment_Donor_Test_NoProK_P5,P4,C564,Tellseq_Shortread_Metagenomic_Analysis_00000,Marine.Sediment.30.32cm.R3,4,
+example_A_R3,example.A.R3,MarineSediment_Donor_Test_NoProK_P5,A5,C565,Tellseq_Shortread_Metagenomic_Analysis_00000,example.A.R3,4,
+Soil_Test_T4_2_Tube5,Soil.Test.T4.2.Tube5,16_member_community_native_soil_P6,B5,C573,Tellseq_Shortread_Metagenomic_Analysis_00000,Soil.Test.T4.2.Tube5,4,
+example_B_R2,example.B.R2,MarineSediment_Donor_Test_NoProK_P5,C5,C566,Tellseq_Shortread_Metagenomic_Analysis_00000,example.B.R2,4,
+A21,A21,Tumor_Community_P7,D5,C574,Tellseq_Shortread_Metagenomic_Analysis_00000,A21,4,
+example_C_R4,example.C.R4,MarineSediment_Donor_Test_NoProK_P5,E5,C567,Tellseq_Shortread_Metagenomic_Analysis_00000,example.C.R4,4,
+A23,A23,Tumor_Community_P7,F5,C575,Tellseq_Shortread_Metagenomic_Analysis_00000,A23,4,
+example_D_R2,example.D.R2,MarineSediment_Donor_Test_NoProK_P5,G5,C568,Tellseq_Shortread_Metagenomic_Analysis_00000,example.D.R2,4,
+A27,A27,Tumor_Community_P7,H5,C576,Tellseq_Shortread_Metagenomic_Analysis_00000,A27,4,
+Soil_Test_T1_2_Tube1,Soil.Test.T1.2.Tube1,16_member_community_native_soil_P6,I5,C569,Tellseq_Shortread_Metagenomic_Analysis_00000,Soil.Test.T1.2.Tube1,4,
+A30,A30,Tumor_Community_P7,J5,C577,Tellseq_Shortread_Metagenomic_Analysis_00000,A30,4,
+Soil_Test_T2_2_Tube2,Soil .Test.T2.2.Tube2,16_member_community_native_soil_P6,K5,C570,Tellseq_Shortread_Metagenomic_Analysis_00000,Soil.Test.T2.2.Tube2,4,
+A31,A31,Tumor_Community_P7,L5,C578,Tellseq_Shortread_Metagenomic_Analysis_00000,A31,4,
+Soil_Test_T3_2_Tube3,Soil.Test.T3.2.Tube3,16_member_community_native_soil_P6,M5,C571,Tellseq_Shortread_Metagenomic_Analysis_00000,Soil.Test.T3.2.Tube3,4,
+Test1_T1_A,Test1.T1.A,Tumor_Community_P7,N5,C579,Tellseq_Shortread_Metagenomic_Analysis_00000,Test1.T1.A,4,
+Soil_Test_T4_1_Tube4,Soil.Test.T4.1.Tube4,16_member_community_native_soil_P6,O5,C572,Tellseq_Shortread_Metagenomic_Analysis_00000,Soil.Test.T4.1.Tube4,4,
+Test2_T1_B_A,Test2.T1.B.A,Tumor_Community_P7,P5,C580,Tellseq_Shortread_Metagenomic_Analysis_00000,Test2.T1.B.A,4,
+Test2_T1_01BH1_Y_A,Test2.T1.01BH1.Y.A,Tumor_Community_P7,A6,C581,Tellseq_Shortread_Metagenomic_Analysis_00000,Test2.T1.01BH1.Y.A,4,
+Test1_T1_1test_A,Test1.T1.1test.A,Tumor_Community_P7,B6,C589,Tellseq_Shortread_Metagenomic_Analysis_00000,Test1.T1.1test.A,4,
+Test2_MT1_1ex_Y_A,Test2.MT1.1ex.Y.A,Tumor_Community_P7,C6,C582,Tellseq_Shortread_Metagenomic_Analysis_00000,Test2.MT1.1ex.Y.A,4,
+Test1_M1_B_1test_A,Test1.M1.B.1test.A,Tumor_Community_P7,D6,C590,Tellseq_Shortread_Metagenomic_Analysis_00000,Test1.M1.B.1test.A,4,
+Test1_T1_B_Sample_A,Test1.T1.B.Sample.A,Tumor_Community_P7,E6,C583,Tellseq_Shortread_Metagenomic_Analysis_00000,Test1.T1.B.Sample.A,4,
+BLANK_K15_test,BLANK.K15.test,Tumor_Community_P7,F6,C591,Tellseq_Shortread_Metagenomic_Analysis_00000,BLANK.K15.test,4,
+Test2_MT1_Sample_A,Test2.MT1.Sample.A,Tumor_Community_P7,G6,C584,Tellseq_Shortread_Metagenomic_Analysis_00000,Test2.MT1.Sample.A,4,
+BLANK_M15_test,BLANK.M15.test,Tumor_Community_P7,H6,C592,Tellseq_Shortread_Metagenomic_Analysis_00000,BLANK.M15.test,4,
+Test2_T1_A,Test2.T1.A,Tumor_Community_P7,I6,C585,Tellseq_Shortread_Metagenomic_Analysis_00000,Test2.T1.A,4,
+BLANK_O15_test,BLANK.O15.test,Tumor_Community_P7,J6,C593,Tellseq_Shortread_Metagenomic_Analysis_00000,BLANK.O15.test,4,
+1test_M_CNTL_A,1test.M.CNTL.A,Tumor_Community_P7,K6,C586,Tellseq_Shortread_Metagenomic_Analysis_00000,1test.M.CNTL.A,4,
+BLANK_A17_test,BLANK.A17.test,Tumor_Community_P7,L6,C594,Tellseq_Shortread_Metagenomic_Analysis_00000,BLANK.A17.test,4,
+1test_G_CNTL_A,1test.G.CNTL.A,Tumor_Community_P7,M6,C587,Tellseq_Shortread_Metagenomic_Analysis_00000,1test.G.CNTL.A,4,
+BLANK_C17_test,BLANK.C17.test,Tumor_Community_P7,N6,C595,Tellseq_Shortread_Metagenomic_Analysis_00000,BLANK.C17.test,4,
+GC_2atest_A,GC.2atest.A,Tumor_Community_P7,O6,C588,Tellseq_Shortread_Metagenomic_Analysis_00000,GC.2atest.A,4,
+BLANK_E17_test,BLANK.E17.test,Tumor_Community_P7,P6,C596,Tellseq_Shortread_Metagenomic_Analysis_00000,BLANK.E17.test,4,
+,,,,,,,,
+[Bioinformatics],,,,,,,,
+Sample_Project,QiitaID,BarcodesAreRC,ForwardAdapter,ReverseAdapter,HumanFiltering,library_construction_protocol,experiment_design_description,contains_replicates
+Tellseq_Shortread_Metagenomic_Analysis_00000,00000,True,GATCGGAAGAGCACACGTCTGAACTCCAGTCAC,GATCGGAAGAGCGTCGTGTAGGGAAAGGAGTGT,True,tellseq,tellseq metagenomics,False
+,,,,,,,,
+[Contact],,,,,,,,
+Sample_Project,Email,,,,,,,
+Tellseq_Shortread_Metagenomic_Analysis_00000,test@gmail.com,,,,,,,
+,,,,,,,,
+[SampleContext],,,,,,,,
+sample_name,sample_type,primary_qiita_study,secondary_qiita_studies,,,,,
+BLANK.K15.test,control blank,00000,,,,,,
+BLANK.M15.test,control blank,00000,,,,,,
+BLANK.O15.test,control blank,00000,,,,,,
+BLANK.A17.test,control blank,00000,,,,,,
+BLANK.C17.test,control blank,00000,,,,,,
+BLANK.E17.test,control blank,00000,,,,,,
+,,,,,,,,
diff --git a/sequence_processing_pipeline/tests/data/tellseq_output/tellread_test.sbatch b/sequence_processing_pipeline/tests/data/tellseq_output/tellread_test.sbatch
index 9dc3ccff..2f2d39cf 100644
--- a/sequence_processing_pipeline/tests/data/tellseq_output/tellread_test.sbatch
+++ b/sequence_processing_pipeline/tests/data/tellseq_output/tellread_test.sbatch
@@ -18,7 +18,7 @@ $HOME/qiita-spots/tellread-release-novaseqX/run_tellread_sing.sh \
     -s $(echo C501,C509,C502,C510,C503,C511,C504,C512,C505,C513,C506,C514,C507,C515,C508,C516,C517,C525,C518,C526,C519,C527,C520,C528,C521,C529,C522,C530,C523,C531,C524,C532,C533,C541,C534,C542,C535,C543,C536,C544,C537,C545,C538,C546,C539,C547,C540,C548,C549,C557,C550,C558,C551,C559,C552,C560,C553,C561,C554,C562,C555,C563,C556,C564,C565,C573,C566,C574,C567,C575,C568,C576,C569,C577,C570,C578,C571,C579,C572,C580,C581,C589,C582,C590,C583,C591,C584,C592,C585,C593,C586,C594,C587,C595,C588,C596 | tr -d '"') \
     -g $(echo NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE,NONE | tr -d '"') \
     -j ${SLURM_JOB_CPUS_PER_NODE}  \
-    -l s_1
+    -l s_4
 
 # get the timestamp for the most recently changed file in directory '.'
 
diff --git a/sequence_processing_pipeline/tests/test_commands.py b/sequence_processing_pipeline/tests/test_commands.py
index bad8e107..cb4d2f5e 100644
--- a/sequence_processing_pipeline/tests/test_commands.py
+++ b/sequence_processing_pipeline/tests/test_commands.py
@@ -122,6 +122,59 @@ def test_demux(self):
             self.assertFalse(os.path.exists(join(tmp, 'a_R1.fastq.gz')))
             self.assertFalse(os.path.exists(join(tmp, 'a_R2.fastq.gz')))
 
+    def test_demux_w_metadata(self):
+        with TemporaryDirectory() as tmp:
+            id_map = [
+                ["1", "a_R1", "a_R2", "Project_12345"],
+                ["2", "b_R1", "b_R2", "Project_12345"]
+            ]
+
+            infile_data = '\n'.join(['@1::MUX::foo/1 BX:Z:TATGACAGATGCGGCCCT',
+                                     'ATGC', '+', '!!!!',
+                                     '@1::MUX::foo/2 BX:Z:TATGACACATGCGGCCCT',
+                                     'ATGC', '+', '!!!!',
+                                     '@1::MUX::bar/1 BX:Z:TATGACAAATGCGGCCCT',
+                                     'ATGC', '+', '!!!!',
+                                     '@1::MUX::bar/2 BX:Z:TATGACACATGCGGCCCT',
+                                     'ATGC', '+', '!!!!',
+                                     '@2::MUX::baz/1 BX:Z:TATGACATATGCGGCCCT',
+                                     'ATGC', '+', '!!!!',
+                                     '@2::MUX::baz/2 BX:Z:TATGACCCATGCGGCCCT',
+                                     'ATGC', '+', '!!!!',
+                                     '@2::MUX::bing/1 BX:Z:TATGAGGCATGCGGCCCT',
+                                     'ATGC', '+', '!!!!',
+                                     '@2::MUX::bing/2 BX:Z:TATGACGCATGCGGCCCT',
+                                     'ATGC', '+', '!!!!',
+                                     ''])
+            infile = io.StringIO(infile_data)
+
+            exp_data_r1 = ['@baz/1 BX:Z:TATGACATATGCGGCCCT',
+                           'ATGC', '+', '!!!!',
+                           '@bing/1 BX:Z:TATGAGGCATGCGGCCCT',
+                           'ATGC', '+', '!!!!']
+            exp_data_r2 = ['@baz/2 BX:Z:TATGACCCATGCGGCCCT',
+                           'ATGC', '+', '!!!!',
+                           '@bing/2 BX:Z:TATGACGCATGCGGCCCT',
+                           'ATGC', '+', '!!!!']
+
+            task = 1
+            maxtask = 2
+
+            demux(id_map, infile, tmp, task, maxtask)
+
+            obs_r1 = gzip.open(join(tmp, 'Project_12345', 'b_R1.fastq.gz'),
+                               'rt').read()
+            obs_r2 = gzip.open(join(tmp, 'Project_12345', 'b_R2.fastq.gz'),
+                               'rt').read()
+            exp = '\n'.join(exp_data_r1) + '\n'
+            self.assertEqual(obs_r1, exp)
+
+            exp = '\n'.join(exp_data_r2) + '\n'
+            self.assertEqual(obs_r2, exp)
+
+            self.assertFalse(os.path.exists(join(tmp, 'a_R1.fastq.gz')))
+            self.assertFalse(os.path.exists(join(tmp, 'a_R2.fastq.gz')))
+
 
 if __name__ == '__main__':
     unittest.main()
diff --git a/sequence_processing_pipeline/util.py b/sequence_processing_pipeline/util.py
index 6a0781b5..9bec0ebf 100644
--- a/sequence_processing_pipeline/util.py
+++ b/sequence_processing_pipeline/util.py
@@ -68,7 +68,6 @@ def iter_paired_files(files):
                 # using find(), r1_prefix and r2_prefix will be the following:
                 # r1_prefix will be: LS_8_22_2014
                 # r2_prefix will be: LS_8_22_2014_R1_SRE_S3_L007
-
                 r1_prefix = r1_fp[:r1_fp.rfind(r1_exp)]
                 r2_prefix = r2_fp[:r2_fp.rfind(r2_exp)]
 
diff --git a/setup.py b/setup.py
index 39ca4569..0efab6f7 100644
--- a/setup.py
+++ b/setup.py
@@ -42,8 +42,7 @@
           },
       install_requires=[
         'click', 'requests', 'pandas', 'flake8', 'nose', 'coverage',
-        'pgzip', 'jinja2',
-        'metapool @ https://github.com/biocore/'
+        'pgzip', 'jinja2', 'metapool @ https://github.com/biocore/'
         'metagenomics_pooling_notebook/archive/master.zip'
         ],
       entry_points={