[2024-01-24 10:47:24,695] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:24,697] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:24,697] [INFO] DQC Reference Directory: /var/lib/cwl/stg2732f615-c0f8-4765-906e-6d4763f2ceb5/dqc_reference
[2024-01-24 10:47:26,651] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:26,652] [INFO] Task started: Prodigal
[2024-01-24 10:47:26,652] [INFO] Running command: gunzip -c /var/lib/cwl/stg24888770-d608-48b6-84fa-cde1c0399ff0/GCF_019084545.1_ASM1908454v1_genomic.fna.gz | prodigal -d GCF_019084545.1_ASM1908454v1_genomic.fna/cds.fna -a GCF_019084545.1_ASM1908454v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:40,026] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:40,026] [INFO] Task started: HMMsearch
[2024-01-24 10:47:40,026] [INFO] Running command: hmmsearch --tblout GCF_019084545.1_ASM1908454v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2732f615-c0f8-4765-906e-6d4763f2ceb5/dqc_reference/reference_markers.hmm GCF_019084545.1_ASM1908454v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:40,324] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:40,325] [INFO] Found 6/6 markers.
[2024-01-24 10:47:40,372] [INFO] Query marker FASTA was written to GCF_019084545.1_ASM1908454v1_genomic.fna/markers.fasta
[2024-01-24 10:47:40,372] [INFO] Task started: Blastn
[2024-01-24 10:47:40,373] [INFO] Running command: blastn -query GCF_019084545.1_ASM1908454v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2732f615-c0f8-4765-906e-6d4763f2ceb5/dqc_reference/reference_markers.fasta -out GCF_019084545.1_ASM1908454v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:41,210] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:41,215] [INFO] Selected 19 target genomes.
[2024-01-24 10:47:41,215] [INFO] Target genome list was writen to GCF_019084545.1_ASM1908454v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:41,223] [INFO] Task started: fastANI
[2024-01-24 10:47:41,223] [INFO] Running command: fastANI --query /var/lib/cwl/stg24888770-d608-48b6-84fa-cde1c0399ff0/GCF_019084545.1_ASM1908454v1_genomic.fna.gz --refList GCF_019084545.1_ASM1908454v1_genomic.fna/target_genomes.txt --output GCF_019084545.1_ASM1908454v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:57,717] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:57,717] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2732f615-c0f8-4765-906e-6d4763f2ceb5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:57,717] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2732f615-c0f8-4765-906e-6d4763f2ceb5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:57,732] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:47:57,732] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:57,733] [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
Marinobacterium ramblicola	strain=D7	GCA_019084545.1	2849041	2849041	type	True	100.0	1593	1598	95	conclusive
Marinobacterium zhoushanense	strain=CGMCC 1.15341	GCA_014641945.1	1679163	1679163	type	True	87.0513	1231	1598	95	below_threshold
Marinobacterium lutimaris	strain=DSM 22012	GCA_900108065.1	568106	568106	type	True	80.1732	665	1598	95	below_threshold
Marinobacterium mangrovicola	strain=DSM 27697	GCA_004339595.1	1476959	1476959	type	True	80.0579	631	1598	95	below_threshold
Marinobacterium litorale	strain=DSM 23545	GCA_000428985.1	404770	404770	type	True	79.5776	504	1598	95	below_threshold
Marinobacterium arenosum	strain=CAU 1594	GCA_019795155.1	2862496	2862496	type	True	79.5124	472	1598	95	below_threshold
Marinobacterium stanieri	strain=DSM 7027	GCA_900155945.1	49186	49186	type	True	78.4993	359	1598	95	below_threshold
Marinobacterium georgiense	strain=DSM 11526	GCA_900107855.1	48076	48076	type	True	78.3845	308	1598	95	below_threshold
Marinobacterium halophilum	strain=DSM 17586	GCA_003014615.1	267374	267374	type	True	78.3637	340	1598	95	below_threshold
Marinobacterium aestuarii	strain=ST58-10	GCA_001651805.1	1821621	1821621	type	True	77.9678	323	1598	95	below_threshold
Marinobacterium rhizophilum	strain=DSM 18822	GCA_000378045.1	420402	420402	type	True	77.8694	344	1598	95	below_threshold
Marinobacterium profundum	strain=PAMC 27536	GCA_001528745.1	1714300	1714300	type	True	77.7639	268	1598	95	below_threshold
Motiliproteus coralliicola	strain=C34	GCA_003345655.1	2283196	2283196	type	True	77.53	228	1598	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	77.5167	263	1598	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	77.3549	217	1598	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	77.3159	199	1598	95	below_threshold
Halomonas alkalisoli	strain=M5N1S17	GCA_021412585.1	2907158	2907158	type	True	77.2831	184	1598	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	77.2749	222	1598	95	below_threshold
Marinobacter lutaoensis	strain=T5054	GCA_001981305.1	135739	135739	type	True	77.1384	132	1598	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:57,737] [INFO] DFAST Taxonomy check result was written to GCF_019084545.1_ASM1908454v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:57,737] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:57,737] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:57,738] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2732f615-c0f8-4765-906e-6d4763f2ceb5/dqc_reference/checkm_data
[2024-01-24 10:47:57,739] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:57,790] [INFO] Task started: CheckM
[2024-01-24 10:47:57,790] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019084545.1_ASM1908454v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019084545.1_ASM1908454v1_genomic.fna/checkm_input GCF_019084545.1_ASM1908454v1_genomic.fna/checkm_result
[2024-01-24 10:48:39,301] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:39,303] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:39,332] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:39,332] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:39,333] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019084545.1_ASM1908454v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:39,333] [INFO] Task started: Blastn
[2024-01-24 10:48:39,333] [INFO] Running command: blastn -query GCF_019084545.1_ASM1908454v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2732f615-c0f8-4765-906e-6d4763f2ceb5/dqc_reference/reference_markers_gtdb.fasta -out GCF_019084545.1_ASM1908454v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:40,621] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:40,625] [INFO] Selected 9 target genomes.
[2024-01-24 10:48:40,626] [INFO] Target genome list was writen to GCF_019084545.1_ASM1908454v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:40,632] [INFO] Task started: fastANI
[2024-01-24 10:48:40,632] [INFO] Running command: fastANI --query /var/lib/cwl/stg24888770-d608-48b6-84fa-cde1c0399ff0/GCF_019084545.1_ASM1908454v1_genomic.fna.gz --refList GCF_019084545.1_ASM1908454v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019084545.1_ASM1908454v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:49,342] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:49,356] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:49,356] [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_019084545.1	s__Marinobacterium sp019084545	100.0	1593	1598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014641945.1	s__Marinobacterium zhoushanense	87.0503	1231	1598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000705555.1	s__Marinobacterium sp000705555	82.2875	874	1598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	98.11	98.11	0.90	0.90	2	-
GCA_003250495.1	s__Marinobacterium sp003250495	81.0053	503	1598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108065.1	s__Marinobacterium lutimaris	80.1664	666	1598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339595.1	s__Marinobacterium mangrovicola	80.0246	636	1598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000428985.1	s__Marinobacterium litorale	79.57	506	1598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	97.80	97.80	0.87	0.87	2	-
GCF_003345655.1	s__Motiliproteus coralliicola	77.5392	228	1598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Motiliproteus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003315345.1	s__Marinobacter pelagius_A	77.0449	146	1598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:49,359] [INFO] GTDB search result was written to GCF_019084545.1_ASM1908454v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:49,360] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:49,366] [INFO] DFAST_QC result json was written to GCF_019084545.1_ASM1908454v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:49,366] [INFO] DFAST_QC completed!
[2024-01-24 10:48:49,366] [INFO] Total running time: 0h1m25s