[2024-01-24 13:17:44,529] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:44,531] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:44,531] [INFO] DQC Reference Directory: /var/lib/cwl/stg1e1e7685-080e-4140-9f3f-587a81c66bbc/dqc_reference
[2024-01-24 13:17:45,811] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:45,812] [INFO] Task started: Prodigal
[2024-01-24 13:17:45,812] [INFO] Running command: gunzip -c /var/lib/cwl/stg86ece937-a3b5-4d1e-8c01-148970b6a99d/GCF_003721275.1_ASM372127v1_genomic.fna.gz | prodigal -d GCF_003721275.1_ASM372127v1_genomic.fna/cds.fna -a GCF_003721275.1_ASM372127v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:56,110] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:56,110] [INFO] Task started: HMMsearch
[2024-01-24 13:17:56,111] [INFO] Running command: hmmsearch --tblout GCF_003721275.1_ASM372127v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1e1e7685-080e-4140-9f3f-587a81c66bbc/dqc_reference/reference_markers.hmm GCF_003721275.1_ASM372127v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:56,481] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:56,483] [INFO] Found 6/6 markers.
[2024-01-24 13:17:56,519] [INFO] Query marker FASTA was written to GCF_003721275.1_ASM372127v1_genomic.fna/markers.fasta
[2024-01-24 13:17:56,520] [INFO] Task started: Blastn
[2024-01-24 13:17:56,520] [INFO] Running command: blastn -query GCF_003721275.1_ASM372127v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e1e7685-080e-4140-9f3f-587a81c66bbc/dqc_reference/reference_markers.fasta -out GCF_003721275.1_ASM372127v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:57,307] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:57,311] [INFO] Selected 12 target genomes.
[2024-01-24 13:17:57,311] [INFO] Target genome list was writen to GCF_003721275.1_ASM372127v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:57,318] [INFO] Task started: fastANI
[2024-01-24 13:17:57,318] [INFO] Running command: fastANI --query /var/lib/cwl/stg86ece937-a3b5-4d1e-8c01-148970b6a99d/GCF_003721275.1_ASM372127v1_genomic.fna.gz --refList GCF_003721275.1_ASM372127v1_genomic.fna/target_genomes.txt --output GCF_003721275.1_ASM372127v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:10,274] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:10,275] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1e1e7685-080e-4140-9f3f-587a81c66bbc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:10,275] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1e1e7685-080e-4140-9f3f-587a81c66bbc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:10,291] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:18:10,291] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:10,291] [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
Marinomonas rhizomae	strain=IVIA-Po-145	GCA_003721275.1	491948	491948	type	True	100.0	1444	1446	95	conclusive
Marinomonas rhizomae	strain=CECT 7377	GCA_003315485.1	491948	491948	type	True	99.9977	1446	1446	95	conclusive
Marinomonas polaris	strain=DSM 16579	GCA_900129155.1	293552	293552	type	True	85.0372	1052	1446	95	below_threshold
Marinomonas lutimaris	strain=E165	GCA_019426345.1	2846746	2846746	type	True	84.4618	1000	1446	95	below_threshold
Marinomonas foliarum	strain=CECT 7731	GCA_003337275.1	491950	491950	type	True	82.7251	843	1446	95	below_threshold
Marinomonas arctica	strain=328	GCA_003259225.1	383750	383750	type	True	81.5089	778	1446	95	below_threshold
Marinomonas shanghaiensis	strain=DSL-35	GCA_003259175.1	2202418	2202418	type	True	81.3436	780	1446	95	below_threshold
Marinomonas profundi	strain=M1K-6	GCA_012584435.1	2726122	2726122	type	True	81.3124	683	1446	95	below_threshold
Marinomonas primoryensis	strain=MPKMM3633	GCA_013372285.1	178399	178399	type	True	80.3689	730	1446	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:10,301] [INFO] DFAST Taxonomy check result was written to GCF_003721275.1_ASM372127v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:10,302] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:10,303] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:10,303] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1e1e7685-080e-4140-9f3f-587a81c66bbc/dqc_reference/checkm_data
[2024-01-24 13:18:10,306] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:10,352] [INFO] Task started: CheckM
[2024-01-24 13:18:10,353] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003721275.1_ASM372127v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003721275.1_ASM372127v1_genomic.fna/checkm_input GCF_003721275.1_ASM372127v1_genomic.fna/checkm_result
[2024-01-24 13:18:48,827] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:48,828] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:48,849] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:48,849] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:48,850] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003721275.1_ASM372127v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:48,850] [INFO] Task started: Blastn
[2024-01-24 13:18:48,850] [INFO] Running command: blastn -query GCF_003721275.1_ASM372127v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e1e7685-080e-4140-9f3f-587a81c66bbc/dqc_reference/reference_markers_gtdb.fasta -out GCF_003721275.1_ASM372127v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:49,960] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:49,963] [INFO] Selected 8 target genomes.
[2024-01-24 13:18:49,964] [INFO] Target genome list was writen to GCF_003721275.1_ASM372127v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:49,967] [INFO] Task started: fastANI
[2024-01-24 13:18:49,968] [INFO] Running command: fastANI --query /var/lib/cwl/stg86ece937-a3b5-4d1e-8c01-148970b6a99d/GCF_003721275.1_ASM372127v1_genomic.fna.gz --refList GCF_003721275.1_ASM372127v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003721275.1_ASM372127v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:58,033] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:58,041] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:58,042] [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_003315485.1	s__Marinomonas rhizomae	99.9977	1446	1446	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_900129155.1	s__Marinomonas polaris	85.0329	1052	1446	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	97.53	97.35	0.90	0.88	9	-
GCF_018336955.1	s__Marinomonas sp018336955	84.468	1008	1446	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000017285.1	s__Marinomonas sp000017285	84.0368	1042	1446	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	98.39	98.39	0.88	0.88	2	-
GCF_003337275.1	s__Marinomonas foliarum	82.7183	844	1446	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	98.18	98.18	0.87	0.87	2	-
GCF_003259225.1	s__Marinomonas arctica	81.5173	777	1446	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	100.00	100.00	1.00	1.00	3	-
GCF_003259175.1	s__Marinomonas shanghaiensis	81.3436	780	1446	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012584435.1	s__Marinomonas sp012584435	81.3027	684	1446	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:58,044] [INFO] GTDB search result was written to GCF_003721275.1_ASM372127v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:58,044] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:58,047] [INFO] DFAST_QC result json was written to GCF_003721275.1_ASM372127v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:58,048] [INFO] DFAST_QC completed!
[2024-01-24 13:18:58,048] [INFO] Total running time: 0h1m14s