[2024-01-24 12:23:04,415] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:04,416] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:04,416] [INFO] DQC Reference Directory: /var/lib/cwl/stgc386674a-76f2-47a4-b0b3-9ed32ea83842/dqc_reference
[2024-01-24 12:23:05,692] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:05,693] [INFO] Task started: Prodigal
[2024-01-24 12:23:05,693] [INFO] Running command: gunzip -c /var/lib/cwl/stg22d0f4bc-706a-4ebe-aaf6-1339b78c031d/GCF_023502425.1_ASM2350242v1_genomic.fna.gz | prodigal -d GCF_023502425.1_ASM2350242v1_genomic.fna/cds.fna -a GCF_023502425.1_ASM2350242v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:25,224] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:25,225] [INFO] Task started: HMMsearch
[2024-01-24 12:23:25,225] [INFO] Running command: hmmsearch --tblout GCF_023502425.1_ASM2350242v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc386674a-76f2-47a4-b0b3-9ed32ea83842/dqc_reference/reference_markers.hmm GCF_023502425.1_ASM2350242v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:25,502] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:25,503] [INFO] Found 6/6 markers.
[2024-01-24 12:23:25,543] [INFO] Query marker FASTA was written to GCF_023502425.1_ASM2350242v1_genomic.fna/markers.fasta
[2024-01-24 12:23:25,543] [INFO] Task started: Blastn
[2024-01-24 12:23:25,544] [INFO] Running command: blastn -query GCF_023502425.1_ASM2350242v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc386674a-76f2-47a4-b0b3-9ed32ea83842/dqc_reference/reference_markers.fasta -out GCF_023502425.1_ASM2350242v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:26,194] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:26,197] [INFO] Selected 24 target genomes.
[2024-01-24 12:23:26,198] [INFO] Target genome list was writen to GCF_023502425.1_ASM2350242v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:26,206] [INFO] Task started: fastANI
[2024-01-24 12:23:26,207] [INFO] Running command: fastANI --query /var/lib/cwl/stg22d0f4bc-706a-4ebe-aaf6-1339b78c031d/GCF_023502425.1_ASM2350242v1_genomic.fna.gz --refList GCF_023502425.1_ASM2350242v1_genomic.fna/target_genomes.txt --output GCF_023502425.1_ASM2350242v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:41,037] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:41,038] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc386674a-76f2-47a4-b0b3-9ed32ea83842/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:41,038] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc386674a-76f2-47a4-b0b3-9ed32ea83842/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:41,060] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:23:41,060] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:23:41,061] [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 algicola	strain=AsT0115	GCA_005937185.1	2583815	2583815	type	True	78.8402	493	1233	95	below_threshold
Muricauda flava	strain=DSM 22638	GCA_900129665.1	570519	570519	type	True	78.2794	397	1233	95	below_threshold
Muricauda onchidii	strain=XY-359	GCA_004804315.1	2562684	2562684	type	True	78.0468	324	1233	95	below_threshold
Muricauda parva	strain=DSM 25885	GCA_900215465.1	1247520	1247520	type	True	77.949	339	1233	95	below_threshold
Muricauda nanhaiensis	strain=SM1704	GCA_003382275.1	2292706	2292706	type	True	77.8174	283	1233	95	below_threshold
Muricauda ruestringensis	strain=DSM 13258	GCA_000224085.1	111501	111501	type	True	77.7581	211	1233	95	below_threshold
Muricauda beolgyonensis	strain=KCTC 23501	GCA_003992615.1	864064	864064	type	True	77.6724	200	1233	95	below_threshold
Muricauda maritima	strain=72	GCA_003584135.1	2306998	2306998	type	True	77.6613	210	1233	95	below_threshold
Muricauda maritima	strain=72	GCA_008017365.1	2306998	2306998	type	True	77.6613	210	1233	95	below_threshold
Muricauda amphidinii	strain=LMIT004	GCA_013090115.1	2735167	2735167	type	True	77.6526	300	1233	95	below_threshold
Muricauda zhangzhouensis	strain=CGMCC 1.11028	GCA_900102925.1	1073328	1073328	type	True	77.5303	246	1233	95	below_threshold
Muricauda aurea	strain=BC31-1-A7	GCA_017313785.1	2915619	2915619	type	True	77.4741	204	1233	95	below_threshold
Muricauda oceani	strain=501str8	GCA_011068285.1	2698672	2698672	type	True	77.4506	209	1233	95	below_threshold
Muricauda zhangzhouensis	strain=DSM 25030	GCA_900106825.1	1073328	1073328	type	True	77.4285	253	1233	95	below_threshold
Muricauda oceani	strain=501str8	GCA_019457985.1	2698672	2698672	type	True	77.421	211	1233	95	below_threshold
Muricauda pacifica	strain=DSM 25027	GCA_003001695.1	1080225	1080225	type	True	77.4027	235	1233	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	76.4677	59	1233	95	below_threshold
Zobellia barbeyronii	strain=KMM 6746	GCA_018603515.1	2748009	2748009	type	True	76.449	87	1233	95	below_threshold
Poritiphilus flavus	strain=R33	GCA_009901585.1	2697053	2697053	type	True	76.3869	90	1233	95	below_threshold
Maribacter aquivivus	strain=DSM 16478	GCA_900142175.1	228958	228958	type	True	76.3837	95	1233	95	below_threshold
Maribacter polysiphoniae	strain=KCTC 22021	GCA_014673435.1	429344	429344	type	True	76.3392	102	1233	95	below_threshold
Maribacter polysiphoniae	strain=DSM 23514	GCA_003148665.1	429344	429344	type	True	76.2961	100	1233	95	below_threshold
Cellulophaga tyrosinoxydans	strain=DSM 21164	GCA_900176415.1	504486	504486	type	True	76.0752	94	1233	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:41,063] [INFO] DFAST Taxonomy check result was written to GCF_023502425.1_ASM2350242v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:41,063] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:41,063] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:41,064] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc386674a-76f2-47a4-b0b3-9ed32ea83842/dqc_reference/checkm_data
[2024-01-24 12:23:41,065] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:41,106] [INFO] Task started: CheckM
[2024-01-24 12:23:41,106] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023502425.1_ASM2350242v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023502425.1_ASM2350242v1_genomic.fna/checkm_input GCF_023502425.1_ASM2350242v1_genomic.fna/checkm_result
[2024-01-24 12:24:35,960] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:35,962] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:35,982] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:35,982] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:35,983] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023502425.1_ASM2350242v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:35,983] [INFO] Task started: Blastn
[2024-01-24 12:24:35,983] [INFO] Running command: blastn -query GCF_023502425.1_ASM2350242v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc386674a-76f2-47a4-b0b3-9ed32ea83842/dqc_reference/reference_markers_gtdb.fasta -out GCF_023502425.1_ASM2350242v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:36,826] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:36,830] [INFO] Selected 24 target genomes.
[2024-01-24 12:24:36,830] [INFO] Target genome list was writen to GCF_023502425.1_ASM2350242v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:36,847] [INFO] Task started: fastANI
[2024-01-24 12:24:36,848] [INFO] Running command: fastANI --query /var/lib/cwl/stg22d0f4bc-706a-4ebe-aaf6-1339b78c031d/GCF_023502425.1_ASM2350242v1_genomic.fna.gz --refList GCF_023502425.1_ASM2350242v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023502425.1_ASM2350242v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:54,753] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:54,778] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:24:54,778] [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_005937185.1	s__Muricauda algicola	78.8402	493	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129665.1	s__Muricauda flava	78.2794	397	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008040165.1	s__Muricauda hymeniacidonis	78.0574	321	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004804315.1	s__Muricauda sp004804315	78.0366	325	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010993855.1	s__Muricauda sp010993855	77.9868	332	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215465.1	s__Muricauda pacifica_A	77.9393	340	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014698935.1	s__Muricauda sp014698935	77.9323	327	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003382275.1	s__Muricauda nanhaiensis	77.8174	283	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010993815.1	s__Muricauda sp010993815	77.8057	270	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003149745.1	s__Muricauda koreensis	77.7663	319	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001413955.1	s__Muricauda eckloniae	77.7404	289	1233	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	77.6724	200	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003584135.1	s__Muricauda sp003584135	77.6613	210	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	0.99	0.99	2	-
GCF_013090115.1	s__Muricauda amphidinii	77.6526	300	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813125.1	s__Muricauda sp002813125	77.5883	216	1233	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	77.5882	217	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	99.01	99.01	0.89	0.89	2	-
GCF_010468565.1	s__Muricauda sp010468565	77.5583	212	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102925.1	s__Muricauda zhangzhouensis	77.5303	246	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001683915.1	s__Muricauda sp001683915	77.5198	246	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	99.66	99.66	0.95	0.95	2	-
GCF_011068285.1	s__Muricauda sp011068285	77.4506	209	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002167435.2	s__Muricauda sp002167435	77.3571	224	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222835.1	s__Muricauda sp018222835	77.1978	201	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001145.1	s__Croceitalea sp013001145	76.7049	119	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Croceitalea	95.0	99.20	99.17	0.87	0.85	5	-
GCF_003148665.1	s__Maribacter_A polysiphoniae	76.2961	100	1233	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	99.27	98.55	0.95	0.91	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:54,780] [INFO] GTDB search result was written to GCF_023502425.1_ASM2350242v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:54,780] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:54,785] [INFO] DFAST_QC result json was written to GCF_023502425.1_ASM2350242v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:54,785] [INFO] DFAST_QC completed!
[2024-01-24 12:24:54,785] [INFO] Total running time: 0h1m50s