[Mon Dec 19 12:30:27 2022] TRUST4 begins.
[Mon Dec 19 12:30:27 2022] SYSTEM CALL: /home/dong/nice_env/TRUST4-master131222/bam-extractor -b C_102_0029_chr14.tagged.bam -t 24 -f /home/dong/nice_env/TRUST4-master131222/hg38_chr14_bcr.fa -o trust4/C_102_0029_longRead_toassemble  --barcode CB --UMI UB
[Mon Dec 19 12:30:27 2022] Start to extract candidate reads from bam file.
[Mon Dec 19 12:31:57 2022] Finish extracting reads.
[Mon Dec 19 12:31:57 2022] SYSTEM CALL: /home/dong/nice_env/TRUST4-master131222/trust4  -f /home/dong/nice_env/TRUST4-master131222/hg38_chr14_bcr.fa -t 24 -k 53 --trimLevel 2 --skipMateExtension -o trust4/C_102_0029_longRead -u trust4/C_102_0029_longRead_toassemble.fq --barcode trust4/C_102_0029_longRead_toassemble_bc.fa --UMI trust4/C_102_0029_longRead_toassemble_umi.fa
[Mon Dec 19 12:32:17 2022] Read in and count kmers for 100000 reads.
[Mon Dec 19 12:32:52 2022] Read in and count kmers for 200000 reads.
[Mon Dec 19 12:33:34 2022] Read in and count kmers for 300000 reads.
[Mon Dec 19 12:34:26 2022] Read in and count kmers for 400000 reads.
[Mon Dec 19 12:35:23 2022] Read in and count kmers for 500000 reads.
[Mon Dec 19 12:36:24 2022] Read in and count kmers for 600000 reads.
[Mon Dec 19 12:37:29 2022] Read in and count kmers for 700000 reads.
[Mon Dec 19 12:38:35 2022] Read in and count kmers for 800000 reads.
[Mon Dec 19 12:39:43 2022] Read in and count kmers for 900000 reads.
[Mon Dec 19 12:41:05 2022] Read in and count kmers for 1000000 reads.
[Mon Dec 19 12:42:18 2022] Read in and count kmers for 1100000 reads.
[Mon Dec 19 12:43:32 2022] Read in and count kmers for 1200000 reads.
[Mon Dec 19 12:44:46 2022] Read in and count kmers for 1300000 reads.
[Mon Dec 19 12:46:03 2022] Read in and count kmers for 1400000 reads.
[Mon Dec 19 12:47:22 2022] Read in and count kmers for 1500000 reads.
[Mon Dec 19 12:48:42 2022] Read in and count kmers for 1600000 reads.
[Mon Dec 19 12:50:06 2022] Read in and count kmers for 1700000 reads.
[Mon Dec 19 12:51:29 2022] Read in and count kmers for 1800000 reads.
[Mon Dec 19 12:52:54 2022] Read in and count kmers for 1900000 reads.
[Mon Dec 19 12:54:21 2022] Read in and count kmers for 2000000 reads.
[Mon Dec 19 12:55:25 2022] Read in and count kmers for 2100000 reads.
[Mon Dec 19 12:56:10 2022] Read in and count kmers for 2200000 reads.
[Mon Dec 19 12:56:59 2022] Read in and count kmers for 2300000 reads.
[Mon Dec 19 12:57:34 2022] Read in and count kmers for 2400000 reads.
[Mon Dec 19 12:57:52 2022] Read in and count kmers for 2500000 reads.
[Mon Dec 19 12:58:08 2022] Read in and count kmers for 2600000 reads.
[Mon Dec 19 12:58:24 2022] Read in and count kmers for 2700000 reads.
[Mon Dec 19 12:58:39 2022] Read in and count kmers for 2800000 reads.
[Mon Dec 19 12:58:55 2022] Read in and count kmers for 2900000 reads.
[Mon Dec 19 12:59:14 2022] Read in and count kmers for 3000000 reads.
[Mon Dec 19 12:59:30 2022] Read in and count kmers for 3100000 reads.
[Mon Dec 19 13:37:09 2022] Found 3137630 reads.
[Mon Dec 19 13:38:18 2022] Finish sorting the reads.
[Mon Dec 19 13:45:34 2022] Finish rough annotations.
[Mon Dec 19 13:48:57 2022] Processed 100000 reads (99656 are used for assembly).
[Mon Dec 19 13:57:14 2022] Processed 200000 reads (199143 are used for assembly).
[Mon Dec 19 14:15:53 2022] Processed 300000 reads (298632 are used for assembly).
[Mon Dec 19 14:49:18 2022] Processed 400000 reads (396027 are used for assembly).
[Mon Dec 19 15:40:29 2022] Processed 500000 reads (495769 are used for assembly).
[Mon Dec 19 16:45:48 2022] Processed 600000 reads (595611 are used for assembly).
[Mon Dec 19 18:05:36 2022] Processed 700000 reads (695479 are used for assembly).
[Mon Dec 19 19:11:43 2022] Processed 800000 reads (795326 are used for assembly).
[Mon Dec 19 19:52:53 2022] Processed 900000 reads (895024 are used for assembly).
[Mon Dec 19 20:12:37 2022] Processed 1000000 reads (993744 are used for assembly).
[Mon Dec 19 20:40:54 2022] Processed 1100000 reads (1093530 are used for assembly).
[Mon Dec 19 21:32:32 2022] Processed 1200000 reads (1192878 are used for assembly).
[Mon Dec 19 22:27:30 2022] Processed 1300000 reads (1292568 are used for assembly).
[Mon Dec 19 22:51:58 2022] Processed 1400000 reads (1392090 are used for assembly).
[Mon Dec 19 22:55:49 2022] Assembled 1434448 reads.
[Mon Dec 19 22:55:49 2022] Try to rescue 0 reads for assembly.
[Mon Dec 19 22:55:57 2022] Rescued 0 reads.
[Mon Dec 19 23:10:06 2022] SYSTEM CALL: /home/dong/nice_env/TRUST4-master131222/annotator -f /home/dong/nice_env/TRUST4-master131222/humanIGH_IMGT+C.fa -a trust4/C_102_0029_longRead_final.out -t 24 -o trust4/C_102_0029_longRead --barcode --UMI -r trust4/C_102_0029_longRead_assembled_reads.fa --airrAlignment > trust4/C_102_0029_longRead_annot.fa
[Mon Dec 19 23:10:06 2022] Start to annotate assemblies.
[Mon Dec 19 23:32:28 2022] Start to realign reads for CDR3 analysis.
[Tue Dec 20 03:52:36 2022] Compute CDR3 abundance.
[Tue Dec 20 03:52:44 2022] Finish annotation.
[Tue Dec 20 03:53:15 2022] SYSTEM CALL: perl /home/dong/nice_env/TRUST4-master131222/trust-barcoderep.pl trust4/C_102_0029_longRead_cdr3.out -a trust4/C_102_0029_longRead_annot.fa --chainsInBarcode 2 > trust4/C_102_0029_longRead_barcode_report.tsv
[Tue Dec 20 03:53:38 2022] SYSTEM CALL: perl /home/dong/nice_env/TRUST4-master131222/trust-simplerep.pl trust4/C_102_0029_longRead_cdr3.out  --barcodeCnt --filterBarcoderep trust4/C_102_0029_longRead_barcode_report.tsv > trust4/C_102_0029_longRead_report.tsv
[Tue Dec 20 03:53:49 2022] SYSTEM CALL: perl /home/dong/nice_env/TRUST4-master131222/trust-airr.pl trust4/C_102_0029_longRead_report.tsv trust4/C_102_0029_longRead_annot.fa --airr-align trust4/C_102_0029_longRead_airr_align.tsv > trust4/C_102_0029_longRead_airr.tsv
[Tue Dec 20 03:53:59 2022] SYSTEM CALL: perl /home/dong/nice_env/TRUST4-master131222/trust-airr.pl trust4/C_102_0029_longRead_barcode_report.tsv trust4/C_102_0029_longRead_annot.fa --format barcoderep --airr-align trust4/C_102_0029_longRead_airr_align.tsv > trust4/C_102_0029_longRead_barcode_airr.tsv
[Tue Dec 20 03:54:09 2022] TRUST4 finishes.