[2024-01-24 13:40:43,840] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:43,842] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:43,843] [INFO] DQC Reference Directory: /var/lib/cwl/stg469b1c0f-1328-48f6-9246-a81e8618bc55/dqc_reference
[2024-01-24 13:40:45,212] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:45,213] [INFO] Task started: Prodigal
[2024-01-24 13:40:45,214] [INFO] Running command: gunzip -c /var/lib/cwl/stg91801db6-ca82-4a12-8416-219899bc27eb/GCF_014131675.1_ASM1413167v1_genomic.fna.gz | prodigal -d GCF_014131675.1_ASM1413167v1_genomic.fna/cds.fna -a GCF_014131675.1_ASM1413167v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:54,533] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:54,534] [INFO] Task started: HMMsearch
[2024-01-24 13:40:54,534] [INFO] Running command: hmmsearch --tblout GCF_014131675.1_ASM1413167v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg469b1c0f-1328-48f6-9246-a81e8618bc55/dqc_reference/reference_markers.hmm GCF_014131675.1_ASM1413167v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:54,870] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:54,871] [INFO] Found 6/6 markers.
[2024-01-24 13:40:54,907] [INFO] Query marker FASTA was written to GCF_014131675.1_ASM1413167v1_genomic.fna/markers.fasta
[2024-01-24 13:40:54,908] [INFO] Task started: Blastn
[2024-01-24 13:40:54,908] [INFO] Running command: blastn -query GCF_014131675.1_ASM1413167v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg469b1c0f-1328-48f6-9246-a81e8618bc55/dqc_reference/reference_markers.fasta -out GCF_014131675.1_ASM1413167v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:55,645] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:55,648] [INFO] Selected 8 target genomes.
[2024-01-24 13:40:55,648] [INFO] Target genome list was writen to GCF_014131675.1_ASM1413167v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:55,653] [INFO] Task started: fastANI
[2024-01-24 13:40:55,653] [INFO] Running command: fastANI --query /var/lib/cwl/stg91801db6-ca82-4a12-8416-219899bc27eb/GCF_014131675.1_ASM1413167v1_genomic.fna.gz --refList GCF_014131675.1_ASM1413167v1_genomic.fna/target_genomes.txt --output GCF_014131675.1_ASM1413167v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:04,159] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:04,159] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg469b1c0f-1328-48f6-9246-a81e8618bc55/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:04,160] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg469b1c0f-1328-48f6-9246-a81e8618bc55/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:04,168] [INFO] Found 8 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:41:04,168] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:04,169] [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
Anaerostipes caccae	strain=DSM 14662	GCA_014131675.1	105841	105841	type	True	100.0	1196	1196	95	conclusive
Anaerostipes caccae	strain=JCM 13470	GCA_014467075.1	105841	105841	type	True	99.9967	1196	1196	95	conclusive
Anaerostipes caccae	strain=DSM 14662	GCA_025146005.1	105841	105841	type	True	99.9956	1196	1196	95	conclusive
Anaerostipes caccae	strain=DSM 14662	GCA_000154305.1	105841	105841	type	True	99.9772	1182	1196	95	conclusive
Anaerostipes hominis	strain=BG01	GCA_002270485.1	2025494	2025494	type	True	92.0051	804	1196	95	below_threshold
Anaerostipes rhamnosivorans	strain=1y2	GCA_005280655.1	1229621	1229621	type	True	82.8571	738	1196	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	79.0419	71	1196	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_025149285.1	154046	154046	suspected-type	True	78.7913	71	1196	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:04,170] [INFO] DFAST Taxonomy check result was written to GCF_014131675.1_ASM1413167v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:04,171] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:04,172] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:04,172] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg469b1c0f-1328-48f6-9246-a81e8618bc55/dqc_reference/checkm_data
[2024-01-24 13:41:04,174] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:04,215] [INFO] Task started: CheckM
[2024-01-24 13:41:04,216] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014131675.1_ASM1413167v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014131675.1_ASM1413167v1_genomic.fna/checkm_input GCF_014131675.1_ASM1413167v1_genomic.fna/checkm_result
[2024-01-24 13:41:36,874] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:36,876] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:36,895] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:36,895] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:36,896] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014131675.1_ASM1413167v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:36,896] [INFO] Task started: Blastn
[2024-01-24 13:41:36,896] [INFO] Running command: blastn -query GCF_014131675.1_ASM1413167v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg469b1c0f-1328-48f6-9246-a81e8618bc55/dqc_reference/reference_markers_gtdb.fasta -out GCF_014131675.1_ASM1413167v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:37,982] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:37,985] [INFO] Selected 13 target genomes.
[2024-01-24 13:41:37,985] [INFO] Target genome list was writen to GCF_014131675.1_ASM1413167v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:37,999] [INFO] Task started: fastANI
[2024-01-24 13:41:37,999] [INFO] Running command: fastANI --query /var/lib/cwl/stg91801db6-ca82-4a12-8416-219899bc27eb/GCF_014131675.1_ASM1413167v1_genomic.fna.gz --refList GCF_014131675.1_ASM1413167v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014131675.1_ASM1413167v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:46,181] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:46,200] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:46,200] [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_014467075.1	s__Anaerostipes caccae	99.9967	1196	1196	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes	95.0	98.81	98.30	0.93	0.89	11	conclusive
GCA_000508985.1	s__Anaerostipes sp000508985	92.0514	795	1196	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes	95.0	98.99	98.66	0.91	0.87	11	-
GCF_005280655.1	s__Anaerostipes rhamnosivorans	82.8154	740	1196	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes	95.0	99.93	99.92	0.96	0.94	3	-
GCA_018381315.1	s__Anaerostipes sp018381315	82.2992	754	1196	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016586355.1	s__Anaerostipes butyraticus	77.9052	159	1196	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes	95.0	99.19	99.02	0.93	0.93	4	-
GCA_902362875.1	s__Anaerostipes sp900066705	77.7795	115	1196	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes	95.0	99.16	98.31	0.96	0.92	3	-
GCA_019114985.1	s__Anaerostipes excrementavium	77.5859	128	1196	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes	95.0	99.16	98.38	0.90	0.84	3	-
GCF_001404655.1	s__Anaerostipes hadrus_A	77.3293	101	1196	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes	95.0	99.11	98.66	0.92	0.88	9	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:46,202] [INFO] GTDB search result was written to GCF_014131675.1_ASM1413167v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:46,203] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:46,206] [INFO] DFAST_QC result json was written to GCF_014131675.1_ASM1413167v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:46,206] [INFO] DFAST_QC completed!
[2024-01-24 13:41:46,206] [INFO] Total running time: 0h1m2s