[2024-01-24 14:06:04,742] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:04,744] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:04,744] [INFO] DQC Reference Directory: /var/lib/cwl/stge4360030-d98f-47b5-af1d-7290ea9aef1d/dqc_reference
[2024-01-24 14:06:05,998] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:05,999] [INFO] Task started: Prodigal
[2024-01-24 14:06:05,999] [INFO] Running command: gunzip -c /var/lib/cwl/stgafbab605-ffab-43a9-a47b-c5819fc2c160/GCF_004340925.1_ASM434092v1_genomic.fna.gz | prodigal -d GCF_004340925.1_ASM434092v1_genomic.fna/cds.fna -a GCF_004340925.1_ASM434092v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:22,349] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:22,349] [INFO] Task started: HMMsearch
[2024-01-24 14:06:22,349] [INFO] Running command: hmmsearch --tblout GCF_004340925.1_ASM434092v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge4360030-d98f-47b5-af1d-7290ea9aef1d/dqc_reference/reference_markers.hmm GCF_004340925.1_ASM434092v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:22,760] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:22,761] [INFO] Found 6/6 markers.
[2024-01-24 14:06:22,811] [INFO] Query marker FASTA was written to GCF_004340925.1_ASM434092v1_genomic.fna/markers.fasta
[2024-01-24 14:06:22,812] [INFO] Task started: Blastn
[2024-01-24 14:06:22,812] [INFO] Running command: blastn -query GCF_004340925.1_ASM434092v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge4360030-d98f-47b5-af1d-7290ea9aef1d/dqc_reference/reference_markers.fasta -out GCF_004340925.1_ASM434092v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:23,558] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:23,563] [INFO] Selected 10 target genomes.
[2024-01-24 14:06:23,563] [INFO] Target genome list was writen to GCF_004340925.1_ASM434092v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:23,567] [INFO] Task started: fastANI
[2024-01-24 14:06:23,568] [INFO] Running command: fastANI --query /var/lib/cwl/stgafbab605-ffab-43a9-a47b-c5819fc2c160/GCF_004340925.1_ASM434092v1_genomic.fna.gz --refList GCF_004340925.1_ASM434092v1_genomic.fna/target_genomes.txt --output GCF_004340925.1_ASM434092v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:35,117] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:35,118] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge4360030-d98f-47b5-af1d-7290ea9aef1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:35,118] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge4360030-d98f-47b5-af1d-7290ea9aef1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:35,127] [INFO] Found 10 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 14:06:35,127] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:06:35,127] [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
Blautia coccoides	strain=DSM 935	GCA_004340925.1	1532	1532	type	True	100.0	1944	1949	95	inconclusive
Blautia coccoides	strain=NCTC11035	GCA_900461125.1	1532	1532	type	True	99.9993	1948	1949	95	inconclusive
Blautia producta	strain=DSM 2950	GCA_014131715.1	33035	33035	suspected-type	True	98.043	1589	1949	95	inconclusive
Blautia producta	strain=DSM 2950	GCA_000439125.1	33035	33035	suspected-type	True	98.0052	1581	1949	95	inconclusive
Blautia producta	strain=ATCC 27340	GCA_000373885.1	33035	33035	suspected-type	True	97.9847	1599	1949	95	inconclusive
Blautia marasmi	strain=Marseille-P2377	GCA_900258535.1	1917868	1917868	suspected-type	True	85.042	1351	1949	95	below_threshold
Anaerostipes rhamnosivorans	strain=1y2	GCA_005280655.1	1229621	1229621	type	True	78.0903	51	1949	95	below_threshold
Mediterraneibacter catenae	strain=SW178	GCA_008691045.1	2594882	2594882	type	True	76.837	73	1949	95	below_threshold
Roseburia lenta	strain=NSJ-9	GCA_014287435.1	2763061	2763061	type	True	76.5403	51	1949	95	below_threshold
Diplocloster agilis	strain=ASD5720	GCA_019042275.1	2850323	2850323	type	True	76.5312	79	1949	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:35,129] [INFO] DFAST Taxonomy check result was written to GCF_004340925.1_ASM434092v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:35,130] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:35,130] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:35,130] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge4360030-d98f-47b5-af1d-7290ea9aef1d/dqc_reference/checkm_data
[2024-01-24 14:06:35,131] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:35,190] [INFO] Task started: CheckM
[2024-01-24 14:06:35,190] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004340925.1_ASM434092v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004340925.1_ASM434092v1_genomic.fna/checkm_input GCF_004340925.1_ASM434092v1_genomic.fna/checkm_result
[2024-01-24 14:07:23,425] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:23,427] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:23,449] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:23,450] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:23,450] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004340925.1_ASM434092v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:23,450] [INFO] Task started: Blastn
[2024-01-24 14:07:23,451] [INFO] Running command: blastn -query GCF_004340925.1_ASM434092v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge4360030-d98f-47b5-af1d-7290ea9aef1d/dqc_reference/reference_markers_gtdb.fasta -out GCF_004340925.1_ASM434092v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:24,525] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:24,528] [INFO] Selected 11 target genomes.
[2024-01-24 14:07:24,528] [INFO] Target genome list was writen to GCF_004340925.1_ASM434092v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:24,537] [INFO] Task started: fastANI
[2024-01-24 14:07:24,537] [INFO] Running command: fastANI --query /var/lib/cwl/stgafbab605-ffab-43a9-a47b-c5819fc2c160/GCF_004340925.1_ASM434092v1_genomic.fna.gz --refList GCF_004340925.1_ASM434092v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004340925.1_ASM434092v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:34,395] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:34,412] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:34,413] [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_900461125.1	s__Blautia coccoides	99.9993	1948	1949	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	98.33	97.47	0.84	0.79	11	conclusive
GCF_014287615.1	s__Blautia sp001304935	85.5779	1325	1949	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	99.32	98.73	0.92	0.87	9	-
GCF_001689125.2	s__Blautia pseudococcoides	85.0906	1183	1949	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	99.82	99.56	0.97	0.91	7	-
GCA_002270465.1	s__Blautia hominis	85.0692	1293	1949	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	98.84	98.04	0.89	0.81	4	-
GCA_003481745.1	s__Blautia stercoris	78.4613	214	1949	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	98.69	97.83	0.91	0.84	8	-
GCF_003477525.1	s__Blautia_A sp003477525	78.1286	137	1949	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	99.30	98.60	0.90	0.81	3	-
GCA_902363515.1	s__Blautia sp000432195	77.9039	220	1949	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	98.93	98.81	0.87	0.83	7	-
GCF_002161285.1	s__Blautia ornithocaccae	77.7447	248	1949	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	98.34	98.05	0.87	0.83	4	-
GCA_900765525.1	s__Blautia pullicola	77.7441	195	1949	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	99.10	98.67	0.84	0.76	4	-
GCA_019114495.1	s__Blautia stercoravium	77.5431	187	1949	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:34,415] [INFO] GTDB search result was written to GCF_004340925.1_ASM434092v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:34,415] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:34,420] [INFO] DFAST_QC result json was written to GCF_004340925.1_ASM434092v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:34,420] [INFO] DFAST_QC completed!
[2024-01-24 14:07:34,420] [INFO] Total running time: 0h1m30s