[2023-03-14 15:15:38,715] [INFO] DFAST_QC pipeline started.
[2023-03-14 15:15:38,715] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 15:15:38,716] [INFO] DQC Reference Directory: /var/lib/cwl/stg95a6e350-7d9b-4d27-aeec-bb1d2d3b3c86/dqc_reference
[2023-03-14 15:15:39,821] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 15:15:39,822] [INFO] Task started: Prodigal
[2023-03-14 15:15:39,822] [INFO] Running command: cat /var/lib/cwl/stgdea021fa-25d0-4d22-9054-2a9dc91d9742/OceanDNA-b7327.fa | prodigal -d OceanDNA-b7327/cds.fna -a OceanDNA-b7327/protein.faa -g 11 -q > /dev/null
[2023-03-14 15:15:51,167] [INFO] Task succeeded: Prodigal
[2023-03-14 15:15:51,167] [INFO] Task started: HMMsearch
[2023-03-14 15:15:51,167] [INFO] Running command: hmmsearch --tblout OceanDNA-b7327/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg95a6e350-7d9b-4d27-aeec-bb1d2d3b3c86/dqc_reference/reference_markers.hmm OceanDNA-b7327/protein.faa > /dev/null
[2023-03-14 15:15:51,386] [INFO] Task succeeded: HMMsearch
[2023-03-14 15:15:51,386] [INFO] Found 6/6 markers.
[2023-03-14 15:15:51,398] [INFO] Query marker FASTA was written to OceanDNA-b7327/markers.fasta
[2023-03-14 15:15:51,400] [INFO] Task started: Blastn
[2023-03-14 15:15:51,400] [INFO] Running command: blastn -query OceanDNA-b7327/markers.fasta -db /var/lib/cwl/stg95a6e350-7d9b-4d27-aeec-bb1d2d3b3c86/dqc_reference/reference_markers.fasta -out OceanDNA-b7327/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 15:15:52,153] [INFO] Task succeeded: Blastn
[2023-03-14 15:15:52,153] [INFO] Selected 31 target genomes.
[2023-03-14 15:15:52,154] [INFO] Target genome list was writen to OceanDNA-b7327/target_genomes.txt
[2023-03-14 15:15:52,165] [INFO] Task started: fastANI
[2023-03-14 15:15:52,165] [INFO] Running command: fastANI --query /var/lib/cwl/stgdea021fa-25d0-4d22-9054-2a9dc91d9742/OceanDNA-b7327.fa --refList OceanDNA-b7327/target_genomes.txt --output OceanDNA-b7327/fastani_result.tsv --threads 1
[2023-03-14 15:16:17,879] [INFO] Task succeeded: fastANI
[2023-03-14 15:16:17,880] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg95a6e350-7d9b-4d27-aeec-bb1d2d3b3c86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 15:16:17,880] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg95a6e350-7d9b-4d27-aeec-bb1d2d3b3c86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 15:16:17,945] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 15:16:17,946] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 15:16:17,946] [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
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	76.5813	99	565	95	below_threshold
Algibacter mikhailovii	strain=KCTC 12710	GCA_014651495.1	425498	425498	type	True	76.5151	69	565	95	below_threshold
Bizionia myxarmorum	strain=ADA-4	GCA_008086205.1	291186	291186	type	True	76.5105	74	565	95	below_threshold
Winogradskyella ouciana	strain=ZXX205	GCA_009709615.1	2608631	2608631	type	True	76.3346	64	565	95	below_threshold
Olleya marilimosa	strain=CAM030	GCA_000518485.1	272164	272164	type	True	76.3334	91	565	95	below_threshold
Winogradskyella flava	strain=KCTC 52348	GCA_014243395.1	1884876	1884876	type	True	76.3302	53	565	95	below_threshold
Hanstruepera ponticola	strain=MM-14	GCA_012931685.1	2042995	2042995	type	True	76.2967	75	565	95	below_threshold
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	76.2931	98	565	95	below_threshold
Bizionia argentinensis	strain=JUB59	GCA_000224335.2	456455	456455	type	True	76.2392	73	565	95	below_threshold
Winogradskyella algicola	strain=IMCC33238	GCA_005869935.1	2575815	2575815	type	True	76.2289	69	565	95	below_threshold
Winogradskyella thalassocola	strain=DSM 15363	GCA_900099995.1	262004	262004	type	True	76.2185	100	565	95	below_threshold
Xanthomarina gelatinilytica	strain=AK20	GCA_000348685.1	1137281	1137281	type	True	76.1785	59	565	95	below_threshold
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	76.1729	79	565	95	below_threshold
Formosa haliotis	strain=LMG 28520	GCA_001685485.1	1555194	1555194	type	True	76.162	76	565	95	below_threshold
Winogradskyella undariae	strain=CCUG 63832	GCA_013285155.1	1285465	1285465	type	True	76.1511	80	565	95	below_threshold
Bizionia algoritergicola	strain=APA-1	GCA_008086165.1	291187	291187	type	True	76.1325	75	565	95	below_threshold
Winogradskyella forsetii	strain=HL857	GCA_013394595.1	2686077	2686077	type	True	76.1157	79	565	95	below_threshold
Algibacter aestuarii	strain=KCTC 23449	GCA_006148925.1	912802	912802	type	True	76.107	74	565	95	below_threshold
Winogradskyella wichelsiae	strain=Z738	GCA_013403925.1	2697007	2697007	type	True	76.075	79	565	95	below_threshold
Winogradskyella psychrotolerans	strain=RS-3	GCA_000427335.1	1344585	1344585	type	True	76.0668	93	565	95	below_threshold
Tamlana haliotis	strain=B1N29	GCA_008806375.1	2614804	2614804	type	True	76.0281	69	565	95	below_threshold
Bizionia paragorgiae	strain=DSM 23842	GCA_900107625.1	283786	283786	type	True	75.9687	70	565	95	below_threshold
Winogradskyella endarachnes	strain=HL2-2	GCA_009741275.1	2681965	2681965	type	True	75.9631	86	565	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	75.9591	60	565	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	75.9571	82	565	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	75.8897	61	565	95	below_threshold
Gelidibacter salicanalis	strain=IC162	GCA_007997285.1	291193	291193	type	True	75.8848	63	565	95	below_threshold
Mariniflexile fucanivorans	strain=DSM 18792	GCA_004341235.1	264023	264023	type	True	75.8641	80	565	95	below_threshold
Winogradskyella tangerina	strain=M1309	GCA_003260205.1	2023240	2023240	type	True	75.8236	61	565	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	75.6977	50	565	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 15:16:17,946] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7327/tc_result.tsv
[2023-03-14 15:16:17,946] [INFO] ===== Taxonomy check completed =====
[2023-03-14 15:16:17,946] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 15:16:17,946] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg95a6e350-7d9b-4d27-aeec-bb1d2d3b3c86/dqc_reference/checkm_data
[2023-03-14 15:16:17,947] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 15:16:17,954] [INFO] Task started: CheckM
[2023-03-14 15:16:17,954] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7327/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7327/checkm_input OceanDNA-b7327/checkm_result
[2023-03-14 15:16:58,997] [INFO] Task succeeded: CheckM
[2023-03-14 15:16:58,997] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 15:16:58,999] [INFO] ===== Completeness check finished =====
[2023-03-14 15:16:58,999] [INFO] ===== Start GTDB Search =====
[2023-03-14 15:16:58,999] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7327/markers.fasta)
[2023-03-14 15:16:59,001] [INFO] Task started: Blastn
[2023-03-14 15:16:59,001] [INFO] Running command: blastn -query OceanDNA-b7327/markers.fasta -db /var/lib/cwl/stg95a6e350-7d9b-4d27-aeec-bb1d2d3b3c86/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7327/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 15:17:00,244] [INFO] Task succeeded: Blastn
[2023-03-14 15:17:00,244] [INFO] Selected 8 target genomes.
[2023-03-14 15:17:00,245] [INFO] Target genome list was writen to OceanDNA-b7327/target_genomes_gtdb.txt
[2023-03-14 15:17:00,326] [INFO] Task started: fastANI
[2023-03-14 15:17:00,326] [INFO] Running command: fastANI --query /var/lib/cwl/stgdea021fa-25d0-4d22-9054-2a9dc91d9742/OceanDNA-b7327.fa --refList OceanDNA-b7327/target_genomes_gtdb.txt --output OceanDNA-b7327/fastani_result_gtdb.tsv --threads 1
[2023-03-14 15:17:04,291] [INFO] Task succeeded: fastANI
[2023-03-14 15:17:04,297] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 15:17:04,297] [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
GCA_018608725.1	s__Hel1-33-131 sp018608725	86.6914	442	565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608765.1	s__Hel1-33-131 sp018608765	83.2771	452	565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001735745.1	s__Hel1-33-131 sp001735745	82.471	469	565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018673215.1	s__Hel1-33-131 sp018673215	81.9909	429	565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608735.1	s__Hel1-33-131 sp018608735	79.8241	295	565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479095.1	s__Hel1-33-131 sp905479095	79.7578	337	565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181825.1	s__Hel1-33-131 sp905181825	78.4369	225	565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	99.01	99.01	0.77	0.77	2	-
GCA_018608625.1	s__Hel1-33-131 sp018608625	78.1427	244	565	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	98.93	97.98	0.88	0.82	3	-
--------------------------------------------------------------------------------
[2023-03-14 15:17:04,297] [INFO] GTDB search result was written to OceanDNA-b7327/result_gtdb.tsv
[2023-03-14 15:17:04,297] [INFO] ===== GTDB Search completed =====
[2023-03-14 15:17:04,299] [INFO] DFAST_QC result json was written to OceanDNA-b7327/dqc_result.json
[2023-03-14 15:17:04,300] [INFO] DFAST_QC completed!
[2023-03-14 15:17:04,300] [INFO] Total running time: 0h1m26s