[2024-01-24 14:39:29,901] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:29,903] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:29,903] [INFO] DQC Reference Directory: /var/lib/cwl/stg290c4876-26ff-45e4-93af-47a1207bd28d/dqc_reference
[2024-01-24 14:39:31,120] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:31,121] [INFO] Task started: Prodigal
[2024-01-24 14:39:31,121] [INFO] Running command: gunzip -c /var/lib/cwl/stg9b1afefb-a497-464e-9a4d-da170339b779/GCF_000238375.3_ASM23837v4_genomic.fna.gz | prodigal -d GCF_000238375.3_ASM23837v4_genomic.fna/cds.fna -a GCF_000238375.3_ASM23837v4_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:45,225] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:45,225] [INFO] Task started: HMMsearch
[2024-01-24 14:39:45,225] [INFO] Running command: hmmsearch --tblout GCF_000238375.3_ASM23837v4_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg290c4876-26ff-45e4-93af-47a1207bd28d/dqc_reference/reference_markers.hmm GCF_000238375.3_ASM23837v4_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:45,537] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:45,538] [INFO] Found 6/6 markers.
[2024-01-24 14:39:45,586] [INFO] Query marker FASTA was written to GCF_000238375.3_ASM23837v4_genomic.fna/markers.fasta
[2024-01-24 14:39:45,586] [INFO] Task started: Blastn
[2024-01-24 14:39:45,586] [INFO] Running command: blastn -query GCF_000238375.3_ASM23837v4_genomic.fna/markers.fasta -db /var/lib/cwl/stg290c4876-26ff-45e4-93af-47a1207bd28d/dqc_reference/reference_markers.fasta -out GCF_000238375.3_ASM23837v4_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:46,353] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:46,358] [INFO] Selected 21 target genomes.
[2024-01-24 14:39:46,358] [INFO] Target genome list was writen to GCF_000238375.3_ASM23837v4_genomic.fna/target_genomes.txt
[2024-01-24 14:39:46,368] [INFO] Task started: fastANI
[2024-01-24 14:39:46,368] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b1afefb-a497-464e-9a4d-da170339b779/GCF_000238375.3_ASM23837v4_genomic.fna.gz --refList GCF_000238375.3_ASM23837v4_genomic.fna/target_genomes.txt --output GCF_000238375.3_ASM23837v4_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:40:04,428] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:04,428] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg290c4876-26ff-45e4-93af-47a1207bd28d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:40:04,429] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg290c4876-26ff-45e4-93af-47a1207bd28d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:40:04,450] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:40:04,451] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:40:04,451] [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
Pseudoalteromonas citrea	strain=DSM 8771	GCA_000238375.4	43655	43655	type	True	100.0	1801	1802	95	conclusive
Pseudoalteromonas aurantia	strain=208	GCA_014858725.1	43654	43654	type	True	82.7981	901	1802	95	below_threshold
Pseudoalteromonas amylolytica	strain=JW1	GCA_001854605.1	1859457	1859457	type	True	79.5825	387	1802	95	below_threshold
Pseudoalteromonas caenipelagi	strain=JBTF-M23	GCA_013140855.1	2726988	2726988	type	True	79.4305	380	1802	95	below_threshold
Pseudoalteromonas byunsanensis	strain=JCM 12483	GCA_001854475.1	327939	327939	type	True	79.3968	383	1802	95	below_threshold
Pseudoalteromonas galatheae	strain=S4498	GCA_005886105.2	579562	579562	type	True	79.1965	283	1802	95	below_threshold
Pseudoalteromonas phenolica	strain=KCTC 12086	GCA_001444405.1	161398	161398	suspected-type	True	79.1155	336	1802	95	below_threshold
Pseudoalteromonas phenolica	strain=O-BC30	GCA_014925335.1	161398	161398	suspected-type	True	79.1046	331	1802	95	below_threshold
Pseudoalteromonas tetraodonis	strain=GFC	GCA_002310835.1	43659	43659	suspected-type	True	79.0341	242	1802	95	below_threshold
Pseudoalteromonas lipolytica	strain=CGMCC 1.8499	GCA_900116435.1	570156	570156	suspected-type	True	78.8165	245	1802	95	below_threshold
Pseudoalteromonas lipolytica	strain=LMEB 39	GCA_014925285.1	570156	570156	suspected-type	True	78.8128	252	1802	95	below_threshold
Pseudoalteromonas arctica	strain=A 37-1-2	GCA_000238395.4	394751	394751	type	True	78.6046	258	1802	95	below_threshold
Pseudoalteromonas distincta	strain=ATCC 700518	GCA_000814675.1	77608	77608	type	True	78.5436	246	1802	95	below_threshold
Pseudoalteromonas aliena	strain=SW19	GCA_014905615.1	247523	247523	type	True	78.503	242	1802	95	below_threshold
Pseudoalteromonas tetraodonis	strain=NBRC 103034	GCA_007991235.1	43659	43659	suspected-type	True	78.4286	228	1802	95	below_threshold
Pseudoalteromonas profundi	strain=CGMCC 1.15394	GCA_014642695.1	1774956	1774956	type	True	78.3378	256	1802	95	below_threshold
Pseudoalteromonas neustonica	strain=PAMC 28425	GCA_001653135.1	1840331	1840331	type	True	78.1619	281	1802	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:40:04,453] [INFO] DFAST Taxonomy check result was written to GCF_000238375.3_ASM23837v4_genomic.fna/tc_result.tsv
[2024-01-24 14:40:04,453] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:40:04,454] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:40:04,454] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg290c4876-26ff-45e4-93af-47a1207bd28d/dqc_reference/checkm_data
[2024-01-24 14:40:04,455] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:40:04,516] [INFO] Task started: CheckM
[2024-01-24 14:40:04,516] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000238375.3_ASM23837v4_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000238375.3_ASM23837v4_genomic.fna/checkm_input GCF_000238375.3_ASM23837v4_genomic.fna/checkm_result
[2024-01-24 14:40:54,996] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:54,997] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:40:55,018] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:55,018] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:55,018] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000238375.3_ASM23837v4_genomic.fna/markers.fasta)
[2024-01-24 14:40:55,019] [INFO] Task started: Blastn
[2024-01-24 14:40:55,019] [INFO] Running command: blastn -query GCF_000238375.3_ASM23837v4_genomic.fna/markers.fasta -db /var/lib/cwl/stg290c4876-26ff-45e4-93af-47a1207bd28d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000238375.3_ASM23837v4_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:56,177] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:56,180] [INFO] Selected 10 target genomes.
[2024-01-24 14:40:56,181] [INFO] Target genome list was writen to GCF_000238375.3_ASM23837v4_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:40:56,189] [INFO] Task started: fastANI
[2024-01-24 14:40:56,189] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b1afefb-a497-464e-9a4d-da170339b779/GCF_000238375.3_ASM23837v4_genomic.fna.gz --refList GCF_000238375.3_ASM23837v4_genomic.fna/target_genomes_gtdb.txt --output GCF_000238375.3_ASM23837v4_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:41:07,575] [INFO] Task succeeded: fastANI
[2024-01-24 14:41:07,587] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:41:07,587] [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_000238375.3	s__Pseudoalteromonas citrea	100.0	1800	1802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003590335.1	s__Pseudoalteromonas sp003590335	89.8007	1438	1802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.57	97.56	0.90	0.89	3	-
GCF_005886875.1	s__Pseudoalteromonas aurantia_A	88.646	1216	1802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.47	99.41	0.94	0.93	3	-
GCF_014858725.1	s__Pseudoalteromonas aurantia	82.7821	902	1802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.50	97.26	0.90	0.89	4	-
GCF_009176705.1	s__Pseudoalteromonas sp009176705	79.7738	398	1802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013140855.1	s__Pseudoalteromonas caenipelagi	79.4588	378	1802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002964665.1	s__Pseudoalteromonas sp002964665	79.4295	367	1802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001444405.1	s__Pseudoalteromonas phenolica	79.1485	336	1802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.52	98.61	0.97	0.92	4	-
GCF_000238395.3	s__Pseudoalteromonas arctica	78.5975	260	1802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	96.91	96.03	0.87	0.80	33	-
GCF_001653135.1	s__Pseudoalteromonas neustonica	78.1752	283	1802	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.11	98.62	0.93	0.89	5	-
--------------------------------------------------------------------------------
[2024-01-24 14:41:07,589] [INFO] GTDB search result was written to GCF_000238375.3_ASM23837v4_genomic.fna/result_gtdb.tsv
[2024-01-24 14:41:07,590] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:41:07,593] [INFO] DFAST_QC result json was written to GCF_000238375.3_ASM23837v4_genomic.fna/dqc_result.json
[2024-01-24 14:41:07,593] [INFO] DFAST_QC completed!
[2024-01-24 14:41:07,594] [INFO] Total running time: 0h1m38s