[2023-03-18 07:06:22,044] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:06:22,044] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:06:22,044] [INFO] DQC Reference Directory: /var/lib/cwl/stg650b8fcf-0e14-469c-9f05-f3521fbc44f8/dqc_reference
[2023-03-18 07:06:23,221] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:06:23,222] [INFO] Task started: Prodigal
[2023-03-18 07:06:23,222] [INFO] Running command: cat /var/lib/cwl/stg2a05aef0-b9fe-45ac-8476-390b1c0bb10e/OceanDNA-b10737.fa | prodigal -d OceanDNA-b10737/cds.fna -a OceanDNA-b10737/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:06:47,690] [INFO] Task succeeded: Prodigal
[2023-03-18 07:06:47,691] [INFO] Task started: HMMsearch
[2023-03-18 07:06:47,691] [INFO] Running command: hmmsearch --tblout OceanDNA-b10737/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg650b8fcf-0e14-469c-9f05-f3521fbc44f8/dqc_reference/reference_markers.hmm OceanDNA-b10737/protein.faa > /dev/null
[2023-03-18 07:06:47,923] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:06:47,923] [INFO] Found 6/6 markers.
[2023-03-18 07:06:47,947] [INFO] Query marker FASTA was written to OceanDNA-b10737/markers.fasta
[2023-03-18 07:06:47,947] [INFO] Task started: Blastn
[2023-03-18 07:06:47,947] [INFO] Running command: blastn -query OceanDNA-b10737/markers.fasta -db /var/lib/cwl/stg650b8fcf-0e14-469c-9f05-f3521fbc44f8/dqc_reference/reference_markers.fasta -out OceanDNA-b10737/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:06:48,577] [INFO] Task succeeded: Blastn
[2023-03-18 07:06:48,578] [INFO] Selected 21 target genomes.
[2023-03-18 07:06:48,578] [INFO] Target genome list was writen to OceanDNA-b10737/target_genomes.txt
[2023-03-18 07:06:48,587] [INFO] Task started: fastANI
[2023-03-18 07:06:48,587] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a05aef0-b9fe-45ac-8476-390b1c0bb10e/OceanDNA-b10737.fa --refList OceanDNA-b10737/target_genomes.txt --output OceanDNA-b10737/fastani_result.tsv --threads 1
[2023-03-18 07:07:03,291] [INFO] Task succeeded: fastANI
[2023-03-18 07:07:03,291] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg650b8fcf-0e14-469c-9f05-f3521fbc44f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:07:03,292] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg650b8fcf-0e14-469c-9f05-f3521fbc44f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:07:03,303] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 07:07:03,304] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 07:07:03,304] [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
Yeosuana marina	strain=JLT21	GCA_011762485.1	1565536	1565536	type	True	97.2313	1083	1287	95	conclusive
Yeosuana aromativorans	strain=JCM 12862	GCA_014646655.1	288019	288019	type	True	79.9634	612	1287	95	below_threshold
Confluentibacter sediminis	strain=DSL-48	GCA_003258355.1	2219045	2219045	type	True	78.7512	418	1287	95	below_threshold
Mariniflexile gromovii	strain=KCTC 12570	GCA_017814435.1	362523	362523	type	True	78.2153	406	1287	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	78.0744	384	1287	95	below_threshold
Olleya marilimosa	strain=CAM030	GCA_000518485.1	272164	272164	type	True	78.0275	254	1287	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	78.0253	330	1287	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	77.9439	359	1287	95	below_threshold
Arenitalea lutea	strain=P7-3-5	GCA_000283015.1	1178825	1178825	type	True	77.9307	358	1287	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	77.8879	369	1287	95	below_threshold
Algibacter alginicilyticus	strain=HZ22	GCA_001310225.1	1736674	1736674	type	True	77.8094	375	1287	95	below_threshold
Algibacter lectus	strain=DSM 15365	GCA_900112395.1	221126	221126	type	True	77.7486	353	1287	95	below_threshold
Changchengzhania lutea	strain=SM1355	GCA_006974145.1	2049305	2049305	type	True	77.7151	361	1287	95	below_threshold
Bizionia echini	strain=DSM 23925	GCA_900115185.1	649333	649333	type	True	77.4888	237	1287	95	below_threshold
Hyunsoonleella pacifica	strain=SW033	GCA_004310335.1	1080224	1080224	type	True	77.4581	270	1287	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	77.4395	216	1287	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	77.4227	251	1287	95	below_threshold
Xanthomarina gelatinilytica	strain=AK20	GCA_000348685.1	1137281	1137281	type	True	77.2381	210	1287	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	77.2095	207	1287	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	77.1747	202	1287	95	below_threshold
Psychroserpens jangbogonensis	strain=PAMC 27130	GCA_000797465.1	1484460	1484460	type	True	77.0836	222	1287	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 07:07:03,304] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10737/tc_result.tsv
[2023-03-18 07:07:03,304] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:07:03,304] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:07:03,304] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg650b8fcf-0e14-469c-9f05-f3521fbc44f8/dqc_reference/checkm_data
[2023-03-18 07:07:03,305] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:07:03,310] [INFO] Task started: CheckM
[2023-03-18 07:07:03,310] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10737/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10737/checkm_input OceanDNA-b10737/checkm_result
[2023-03-18 07:08:03,660] [INFO] Task succeeded: CheckM
[2023-03-18 07:08:03,661] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 07:08:03,664] [INFO] ===== Completeness check finished =====
[2023-03-18 07:08:03,664] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:08:03,664] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10737/markers.fasta)
[2023-03-18 07:08:03,664] [INFO] Task started: Blastn
[2023-03-18 07:08:03,664] [INFO] Running command: blastn -query OceanDNA-b10737/markers.fasta -db /var/lib/cwl/stg650b8fcf-0e14-469c-9f05-f3521fbc44f8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10737/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:08:04,552] [INFO] Task succeeded: Blastn
[2023-03-18 07:08:04,553] [INFO] Selected 13 target genomes.
[2023-03-18 07:08:04,553] [INFO] Target genome list was writen to OceanDNA-b10737/target_genomes_gtdb.txt
[2023-03-18 07:08:04,671] [INFO] Task started: fastANI
[2023-03-18 07:08:04,671] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a05aef0-b9fe-45ac-8476-390b1c0bb10e/OceanDNA-b10737.fa --refList OceanDNA-b10737/target_genomes_gtdb.txt --output OceanDNA-b10737/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:08:13,948] [INFO] Task succeeded: fastANI
[2023-03-18 07:08:13,958] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 07:08:13,958] [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_011762485.1	s__Yeosuana marina	97.2499	1082	1287	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Yeosuana	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014646655.1	s__Yeosuana aromativorans	79.9634	612	1287	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Yeosuana	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002441545.1	s__Yeosuana sp002441545	79.6343	591	1287	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Yeosuana	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002784145.1	s__Yeosuana sp002784145	79.4869	514	1287	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Yeosuana	95.0	99.75	99.57	0.88	0.85	11	-
GCF_000789235.1	s__Wocania ichthyoenteri	78.9568	447	1287	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003258355.1	s__Confluentibacter sp003258355	78.7507	419	1287	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Confluentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114265.1	s__Flaviramulus basaltis	78.6933	492	1287	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004791695.1	s__Flavivirga rizhaonensis	78.0836	383	1287	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001971785.1	s__Seonamhaeicola sp001971785	77.8621	382	1287	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001310225.1	s__Algibacter_A alginicilyticus	77.8113	376	1287	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006974145.1	s__Changchengzhania lutea	77.7061	362	1287	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Changchengzhania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008084905.1	s__Xanthomarina maritima	77.7058	283	1287	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002162765.1	s__MAAR01 sp002162765	77.5091	195	1287	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAAR01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 07:08:14,148] [INFO] GTDB search result was written to OceanDNA-b10737/result_gtdb.tsv
[2023-03-18 07:08:14,149] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:08:14,151] [INFO] DFAST_QC result json was written to OceanDNA-b10737/dqc_result.json
[2023-03-18 07:08:14,151] [INFO] DFAST_QC completed!
[2023-03-18 07:08:14,151] [INFO] Total running time: 0h1m52s