[2024-01-24 13:17:15,696] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:15,697] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:15,698] [INFO] DQC Reference Directory: /var/lib/cwl/stgc50d816f-9206-47c6-8623-a59954484d97/dqc_reference
[2024-01-24 13:17:17,063] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:17,064] [INFO] Task started: Prodigal
[2024-01-24 13:17:17,064] [INFO] Running command: gunzip -c /var/lib/cwl/stg42f92aa5-fa45-40aa-aa97-b59d9fd729ec/GCF_001657435.1_ASM165743v1_genomic.fna.gz | prodigal -d GCF_001657435.1_ASM165743v1_genomic.fna/cds.fna -a GCF_001657435.1_ASM165743v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:24,439] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:24,440] [INFO] Task started: HMMsearch
[2024-01-24 13:17:24,440] [INFO] Running command: hmmsearch --tblout GCF_001657435.1_ASM165743v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc50d816f-9206-47c6-8623-a59954484d97/dqc_reference/reference_markers.hmm GCF_001657435.1_ASM165743v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:24,789] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:24,790] [INFO] Found 6/6 markers.
[2024-01-24 13:17:24,836] [INFO] Query marker FASTA was written to GCF_001657435.1_ASM165743v1_genomic.fna/markers.fasta
[2024-01-24 13:17:24,837] [INFO] Task started: Blastn
[2024-01-24 13:17:24,837] [INFO] Running command: blastn -query GCF_001657435.1_ASM165743v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc50d816f-9206-47c6-8623-a59954484d97/dqc_reference/reference_markers.fasta -out GCF_001657435.1_ASM165743v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:25,463] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:25,466] [INFO] Selected 14 target genomes.
[2024-01-24 13:17:25,466] [INFO] Target genome list was writen to GCF_001657435.1_ASM165743v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:25,471] [INFO] Task started: fastANI
[2024-01-24 13:17:25,471] [INFO] Running command: fastANI --query /var/lib/cwl/stg42f92aa5-fa45-40aa-aa97-b59d9fd729ec/GCF_001657435.1_ASM165743v1_genomic.fna.gz --refList GCF_001657435.1_ASM165743v1_genomic.fna/target_genomes.txt --output GCF_001657435.1_ASM165743v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:39,018] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:39,019] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc50d816f-9206-47c6-8623-a59954484d97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:39,019] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc50d816f-9206-47c6-8623-a59954484d97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:39,029] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:17:39,030] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:39,030] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Clostridium saccharobutylicum	strain=DSM 13864	GCA_001657435.1	169679	169679	type	True	100.0	1477	1491	95	conclusive
Clostridium saccharobutylicum	strain=DSM 13864	GCA_000473995.1	169679	169679	type	True	99.9738	1491	1491	95	conclusive
Clostridium gelidum	strain=C5S11	GCA_019977655.1	704125	704125	type	True	80.8961	790	1491	95	below_threshold
Clostridium puniceum	strain=DSM 2619	GCA_002006345.1	29367	29367	type	True	80.8276	694	1491	95	below_threshold
Clostridium beijerinckii	strain=DSM 791	GCA_002006445.1	1520	1520	suspected-type	True	80.6034	657	1491	95	below_threshold
Clostridium diolis	strain=DSM 15410	GCA_008705175.1	223919	223919	suspected-type	True	80.5925	705	1491	95	below_threshold
Clostridium beijerinckii	strain=DSM 791	GCA_018223745.1	1520	1520	suspected-type	True	80.5312	691	1491	95	below_threshold
Clostridium butyricum	strain=DSM 10702	GCA_000409755.1	1492	1492	type	True	79.3646	460	1491	95	below_threshold
Clostridium cagae	strain=Marseille-P4344	GCA_900290265.1	2080751	2080751	type	True	79.1168	434	1491	95	below_threshold
Clostridium weizhouense	strain=YB-6	GCA_019431045.1	2859781	2859781	type	True	78.8521	507	1491	95	below_threshold
Clostridium cibarium	strain=Sa3CVN1	GCA_014836335.1	2762247	2762247	type	True	78.4295	308	1491	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:39,031] [INFO] DFAST Taxonomy check result was written to GCF_001657435.1_ASM165743v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:39,032] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:39,032] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:39,032] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc50d816f-9206-47c6-8623-a59954484d97/dqc_reference/checkm_data
[2024-01-24 13:17:39,033] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:39,080] [INFO] Task started: CheckM
[2024-01-24 13:17:39,080] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001657435.1_ASM165743v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001657435.1_ASM165743v1_genomic.fna/checkm_input GCF_001657435.1_ASM165743v1_genomic.fna/checkm_result
[2024-01-24 13:18:06,117] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:06,118] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:06,135] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:06,135] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:06,136] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001657435.1_ASM165743v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:06,136] [INFO] Task started: Blastn
[2024-01-24 13:18:06,136] [INFO] Running command: blastn -query GCF_001657435.1_ASM165743v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc50d816f-9206-47c6-8623-a59954484d97/dqc_reference/reference_markers_gtdb.fasta -out GCF_001657435.1_ASM165743v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:06,955] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:06,959] [INFO] Selected 15 target genomes.
[2024-01-24 13:18:06,959] [INFO] Target genome list was writen to GCF_001657435.1_ASM165743v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:06,969] [INFO] Task started: fastANI
[2024-01-24 13:18:06,969] [INFO] Running command: fastANI --query /var/lib/cwl/stg42f92aa5-fa45-40aa-aa97-b59d9fd729ec/GCF_001657435.1_ASM165743v1_genomic.fna.gz --refList GCF_001657435.1_ASM165743v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001657435.1_ASM165743v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:21,328] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:21,346] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:21,346] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_000473995.1	s__Clostridium saccharobutylicum	99.9738	1491	1491	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.89	95.82	0.99	0.83	65	conclusive
GCA_003129525.1	s__Clostridium beijerinckii_D	81.1412	686	1491	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002006345.1	s__Clostridium puniceum	80.7886	697	1491	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018223745.1	s__Clostridium beijerinckii	80.5425	692	1491	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	97.01	95.18	0.85	0.79	244	-
GCF_000621745.1	s__Clostridium beijerinckii_A	80.4347	709	1491	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002029255.1	s__Clostridium chromiireducens	80.1769	637	1491	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.07	97.40	0.90	0.87	3	-
GCF_000230835.1	s__Clostridium sp000230835	80.0564	704	1491	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	96.12	96.12	0.82	0.82	2	-
GCF_002760435.1	s__Clostridium sp002760435	80.0475	651	1491	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.99	99.99	0.98	0.98	2	-
GCF_006742065.1	s__Clostridium butyricum	79.4748	471	1491	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.58	97.46	0.89	0.80	64	-
GCA_015058525.1	s__Clostridium butyricum_A	79.3623	314	1491	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012843905.1	s__Clostridium sp012843905	79.3088	409	1491	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900290265.1	s__Clostridium cagae	79.1071	435	1491	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.09	97.56	0.90	0.85	15	-
GCF_001735765.2	s__Clostridium taeniosporum	79.1014	430	1491	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000827935.1	s__Clostridium botulinum_A	78.9142	434	1491	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.05	97.92	0.91	0.85	31	-
GCA_003539755.1	s__Clostridium sp003539755	78.6172	308	1491	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:21,348] [INFO] GTDB search result was written to GCF_001657435.1_ASM165743v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:21,348] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:21,351] [INFO] DFAST_QC result json was written to GCF_001657435.1_ASM165743v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:21,352] [INFO] DFAST_QC completed!
[2024-01-24 13:18:21,352] [INFO] Total running time: 0h1m6s