not working with compressed files

[leomrtns]

Hello! I am having trouble working with compressed files (xz in my case), which used to be automatically detected before. I am using pangolin 4.0.5, and the file has the proper xz suffix.

Here is the full output:

****
Pangolin running in usher mode.
****
Maximum ambiguity allowed is 0.5.
****
Query file:     /usr/users/QIB_fr005/deolivl/Academic/Quadram/021.ncov/220307.react_omicron/05.update_wave19_0404/09.omicron_recombinant_0411/../../00.received/05.w13_19.nonrecombinant.fasta.xz
****
Data files found:
usher_pb:       /usr/users/QIB_fr005/deolivl/local/miniconda3/lib/python3.7/site-packages/pangolin_data/data/lineageTree.pb
****
Job stats:
job                      count    min threads    max threads
---------------------  -------  -------------  -------------
align_to_reference           1              1              1
all                          1              1              1
cache_sequence_assign        1              1              1
create_seq_hash              1              1              1
get_constellations           1              1              1
merged_info                  1              1              1
scorpio                      1              1              1
sequence_qc                  1              1              1
total                        8              1              1

[Wed Apr 13 11:49:28 2022]
Error in rule align_to_reference:
    jobid: 1
    output: /tmp/tmpjt4nustg/alignment.fasta
    log: /tmp/tmpjt4nustg/logs/minimap2_sam.log (check log file(s) for error message)
    shell:

        awk '{ if ($0 !~ /^>/) { gsub("-", "",$0); } print $0; }' "/usr/users/QIB_fr005/deolivl/Academic/Quadram/021.ncov/220307.react_omicron/05.update_wave19_0404/09.omicron_recombinant_0411/../../00.received/05
.w13_19.nonrecombinant.fasta.xz" |         awk '{ { gsub(" ", "_",$0); } { gsub(",", "_",$0); } print $0; }'  |         minimap2 -a -x asm20 --sam-hit-only --secondary=no --score-N=0  -t  1 /usr/users/QIB_fr005/de
olivl/local/miniconda3/lib/python3.7/site-packages/pangolin/data/reference.fasta - -o /tmp/tmpjt4nustg/mapped.sam &> /tmp/tmpjt4nustg/logs/minimap2_sam.log
        gofasta sam toMultiAlign             -s /tmp/tmpjt4nustg/mapped.sam             -t 1             --reference /usr/users/QIB_fr005/deolivl/local/miniconda3/lib/python3.7/site-packages/pangolin/data/referenc
e.fasta             --trimstart 265             --trimend 29674             --trim             --pad > '/tmp/tmpjt4nustg/alignment.fasta'

        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)


Exiting because a job execution failed. Look above for error message

(If I uncompress the file then everything goes smooth)

cheers,
Leo

[pcjentsch]

I'm also having this issue, the contents of minimap2_sam.log:

[M::mm_idx_gen::1.103*0.99] collected minimizers
[M::mm_idx_gen::1.104*0.99] sorted minimizers
[M::main::1.104*0.99] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::1.104*0.99] mid_occ = 50
[M::mm_idx_stat] kmer size: 19; skip: 10; is_hpc: 0; #seq: 1
[M::mm_idx_stat::1.105*0.99] distinct minimizers: 5370 (100.00% are singletons); average occurrences: 1.000; average spacing: 5.569; total length: 29903
[WARNING]�[1;31m empty sequence name in the input.�[0m
[WARNING]�[1;31m failed to parse the FASTA/FASTQ record next to ''. Continue anyway.�[0m
[M::worker_pipeline::1.106*0.99] mapped 6 sequences
[WARNING]�[1;31m failed to parse the FASTA/FASTQ record next to '��U���5?����5���m�ǯ��_�Y�H������x����9NcC֛�z�����hm��#�$�.�_h���Ӄw���~�h|'�\s�*66��V���*L�)���$���}ّ�{;��'�c�˞�9z{��˨"�h�0�L+��0E�H�9����b������0��Y�ǨYS�>������t�ʟ'. Continue anyway.�[0m
[M::worker_pipeline::1.106*0.99] mapped 1 sequences
[WARNING]�[1;31m empty sequence name in the input.�[0m
[WARNING]�[1;31m failed to parse the FASTA/FASTQ record next to '��E8���_O��&���\n�M'. Continue anyway.�[0m
[M::worker_pipeline::1.106*0.99] mapped 5 sequences
[WARNING]�[1;31m failed to parse the first FASTA/FASTQ record. Continue anyway.�[0m
[M::main] Version: 2.24-r1122
[M::main] CMD: minimap2 -a -x asm20 --sam-hit-only --secondary=no --score-N=0 -t 1 -o /home/workaccount/Work/postdoc/phylogeny/./mapped.sam /home/workaccount/.conda/envs/pangolin/lib/python3.8/site-packages/pangolin/data/reference.fasta -
[M::main] Real time: 1.107 sec; CPU: 1.101 sec; Peak RSS: 0.004 GB