[2024-01-24 13:49:33,538] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:33,540] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:33,540] [INFO] DQC Reference Directory: /var/lib/cwl/stga9c586cf-84ea-48b7-a13e-b40dcb8cdf49/dqc_reference
[2024-01-24 13:49:34,905] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:34,905] [INFO] Task started: Prodigal
[2024-01-24 13:49:34,906] [INFO] Running command: gunzip -c /var/lib/cwl/stgd2cba2f9-2bc5-4782-9a02-a035d9b9c1a0/GCF_003058265.1_ASM305826v1_genomic.fna.gz | prodigal -d GCF_003058265.1_ASM305826v1_genomic.fna/cds.fna -a GCF_003058265.1_ASM305826v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:03,142] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:03,142] [INFO] Task started: HMMsearch
[2024-01-24 13:50:03,142] [INFO] Running command: hmmsearch --tblout GCF_003058265.1_ASM305826v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga9c586cf-84ea-48b7-a13e-b40dcb8cdf49/dqc_reference/reference_markers.hmm GCF_003058265.1_ASM305826v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:03,475] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:03,476] [INFO] Found 6/6 markers.
[2024-01-24 13:50:03,518] [INFO] Query marker FASTA was written to GCF_003058265.1_ASM305826v1_genomic.fna/markers.fasta
[2024-01-24 13:50:03,518] [INFO] Task started: Blastn
[2024-01-24 13:50:03,518] [INFO] Running command: blastn -query GCF_003058265.1_ASM305826v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga9c586cf-84ea-48b7-a13e-b40dcb8cdf49/dqc_reference/reference_markers.fasta -out GCF_003058265.1_ASM305826v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:04,151] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:04,155] [INFO] Selected 8 target genomes.
[2024-01-24 13:50:04,155] [INFO] Target genome list was writen to GCF_003058265.1_ASM305826v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:04,158] [INFO] Task started: fastANI
[2024-01-24 13:50:04,159] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2cba2f9-2bc5-4782-9a02-a035d9b9c1a0/GCF_003058265.1_ASM305826v1_genomic.fna.gz --refList GCF_003058265.1_ASM305826v1_genomic.fna/target_genomes.txt --output GCF_003058265.1_ASM305826v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:11,029] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:11,029] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga9c586cf-84ea-48b7-a13e-b40dcb8cdf49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:11,030] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga9c586cf-84ea-48b7-a13e-b40dcb8cdf49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:11,037] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:11,037] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:11,038] [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
Muricauda amoyensis	strain=GCL-11	GCA_003058265.1	2169401	2169401	type	True	100.0	1353	1353	95	conclusive
Muricauda hadalis	strain=MT-229	GCA_007785775.2	2597517	2597517	type	True	90.6167	1058	1353	95	below_threshold
Muricauda taeanensis	strain=JCM 17757	GCA_003584105.1	1005926	1005926	type	True	89.5205	1051	1353	95	below_threshold
Muricauda antarctica	strain=DSM 26351	GCA_900112295.1	1055723	1055723	type	True	89.3641	1042	1353	95	below_threshold
Muricauda antarctica	strain=CGMCC 1.12174	GCA_900142405.1	1055723	1055723	type	True	89.3501	1045	1353	95	below_threshold
Muricauda hymeniacidonis	strain=176CP4-71	GCA_004296335.1	2517819	2517819	type	True	77.5037	198	1353	95	below_threshold
Robertkochia sediminum	strain=1368	GCA_016786255.1	2785326	2785326	type	True	76.4139	50	1353	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:11,039] [INFO] DFAST Taxonomy check result was written to GCF_003058265.1_ASM305826v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:11,040] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:11,040] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:11,040] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga9c586cf-84ea-48b7-a13e-b40dcb8cdf49/dqc_reference/checkm_data
[2024-01-24 13:50:11,041] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:11,096] [INFO] Task started: CheckM
[2024-01-24 13:50:11,097] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003058265.1_ASM305826v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003058265.1_ASM305826v1_genomic.fna/checkm_input GCF_003058265.1_ASM305826v1_genomic.fna/checkm_result
[2024-01-24 13:51:27,876] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:27,877] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:27,898] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:27,899] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:27,899] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003058265.1_ASM305826v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:27,899] [INFO] Task started: Blastn
[2024-01-24 13:51:27,900] [INFO] Running command: blastn -query GCF_003058265.1_ASM305826v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga9c586cf-84ea-48b7-a13e-b40dcb8cdf49/dqc_reference/reference_markers_gtdb.fasta -out GCF_003058265.1_ASM305826v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:28,732] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:28,738] [INFO] Selected 12 target genomes.
[2024-01-24 13:51:28,739] [INFO] Target genome list was writen to GCF_003058265.1_ASM305826v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:29,022] [INFO] Task started: fastANI
[2024-01-24 13:51:29,022] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2cba2f9-2bc5-4782-9a02-a035d9b9c1a0/GCF_003058265.1_ASM305826v1_genomic.fna.gz --refList GCF_003058265.1_ASM305826v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003058265.1_ASM305826v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:38,933] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:38,949] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:38,949] [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_003058265.1	s__Muricauda sp003058265	100.0	1353	1353	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007785775.2	s__Muricauda sp003973595	90.6167	1058	1353	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	98.36	98.36	0.87	0.87	2	-
GCF_003584105.1	s__Muricauda taeanensis	89.5225	1052	1353	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	97.68	97.68	0.85	0.85	3	-
GCF_003584165.1	s__Muricauda sp003584165	81.0616	669	1353	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003584135.1	s__Muricauda sp003584135	80.8184	677	1353	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	0.99	0.99	2	-
GCF_010500845.1	s__Muricauda sediminis	80.2707	680	1353	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003992615.1	s__Muricauda beolgyonensis	79.4884	556	1353	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001683915.1	s__Muricauda sp001683915	79.204	554	1353	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	99.66	99.66	0.95	0.95	2	-
GCF_003385855.1	s__Muricauda sp003385855	78.9155	523	1353	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	97.98	97.98	0.89	0.89	2	-
GCF_009184425.1	s__Muricauda olearia	78.8906	534	1353	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	96.52	96.52	0.87	0.87	2	-
GCF_017313225.1	s__Muricauda sp017313225	78.8638	505	1353	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003992595.1	s__Muricauda sp002452975	78.6577	537	1353	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	99.01	99.01	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:38,951] [INFO] GTDB search result was written to GCF_003058265.1_ASM305826v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:38,952] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:38,959] [INFO] DFAST_QC result json was written to GCF_003058265.1_ASM305826v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:38,960] [INFO] DFAST_QC completed!
[2024-01-24 13:51:38,960] [INFO] Total running time: 0h2m5s