[2023-03-15 07:52:40,421] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:52:40,421] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:52:40,421] [INFO] DQC Reference Directory: /var/lib/cwl/stg0faf7580-9c7e-411f-9452-d62c653a0277/dqc_reference
[2023-03-15 07:52:41,639] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:52:41,639] [INFO] Task started: Prodigal
[2023-03-15 07:52:41,639] [INFO] Running command: cat /var/lib/cwl/stg5f9255bc-ad3d-4e9d-9642-155d60c5a47e/OceanDNA-b10741.fa | prodigal -d OceanDNA-b10741/cds.fna -a OceanDNA-b10741/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:53:03,323] [INFO] Task succeeded: Prodigal
[2023-03-15 07:53:03,323] [INFO] Task started: HMMsearch
[2023-03-15 07:53:03,323] [INFO] Running command: hmmsearch --tblout OceanDNA-b10741/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0faf7580-9c7e-411f-9452-d62c653a0277/dqc_reference/reference_markers.hmm OceanDNA-b10741/protein.faa > /dev/null
[2023-03-15 07:53:03,578] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:53:03,579] [INFO] Found 6/6 markers.
[2023-03-15 07:53:03,601] [INFO] Query marker FASTA was written to OceanDNA-b10741/markers.fasta
[2023-03-15 07:53:03,601] [INFO] Task started: Blastn
[2023-03-15 07:53:03,601] [INFO] Running command: blastn -query OceanDNA-b10741/markers.fasta -db /var/lib/cwl/stg0faf7580-9c7e-411f-9452-d62c653a0277/dqc_reference/reference_markers.fasta -out OceanDNA-b10741/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:53:04,218] [INFO] Task succeeded: Blastn
[2023-03-15 07:53:04,219] [INFO] Selected 22 target genomes.
[2023-03-15 07:53:04,219] [INFO] Target genome list was writen to OceanDNA-b10741/target_genomes.txt
[2023-03-15 07:53:04,227] [INFO] Task started: fastANI
[2023-03-15 07:53:04,227] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f9255bc-ad3d-4e9d-9642-155d60c5a47e/OceanDNA-b10741.fa --refList OceanDNA-b10741/target_genomes.txt --output OceanDNA-b10741/fastani_result.tsv --threads 1
[2023-03-15 07:53:19,738] [INFO] Task succeeded: fastANI
[2023-03-15 07:53:19,738] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0faf7580-9c7e-411f-9452-d62c653a0277/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:53:19,738] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0faf7580-9c7e-411f-9452-d62c653a0277/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:53:19,751] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:53:19,751] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 07:53:19,752] [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	78.9111	470	1082	95	below_threshold
Yeosuana aromativorans	strain=JCM 12862	GCA_014646655.1	288019	288019	type	True	78.2835	429	1082	95	below_threshold
Mariniflexile fucanivorans	strain=DSM 18792	GCA_004341235.1	264023	264023	type	True	78.0538	390	1082	95	below_threshold
Confluentibacter sediminis	strain=DSL-48	GCA_003258355.1	2219045	2219045	type	True	77.891	360	1082	95	below_threshold
Confluentibacter lentus	strain=HJM-3	GCA_002806995.1	1699412	1699412	type	True	77.7948	304	1082	95	below_threshold
Changchengzhania lutea	strain=SM1355	GCA_006974145.1	2049305	2049305	type	True	77.6906	301	1082	95	below_threshold
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	77.661	297	1082	95	below_threshold
Algibacter alginicilyticus	strain=HZ22	GCA_001310225.1	1736674	1736674	type	True	77.6367	297	1082	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	77.5852	305	1082	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	77.4307	254	1082	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	77.4186	312	1082	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	77.3931	332	1082	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	77.2398	262	1082	95	below_threshold
Algibacter mikhailovii	strain=KCTC 12710	GCA_014651495.1	425498	425498	type	True	77.1879	233	1082	95	below_threshold
Flavivirga eckloniae	strain=ECD14	GCA_002886045.1	1803846	1803846	type	True	77.1409	261	1082	95	below_threshold
Snuella sedimenti	strain=CAU 1569	GCA_016428595.1	2798802	2798802	type	True	77.1274	226	1082	95	below_threshold
Tamlana agarivorans	strain=JW-26	GCA_001642835.1	481183	481183	type	True	77.0023	223	1082	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	76.8445	205	1082	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	76.7846	192	1082	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	76.7589	188	1082	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	76.666	188	1082	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	76.5978	222	1082	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 07:53:19,789] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10741/tc_result.tsv
[2023-03-15 07:53:19,789] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:53:19,789] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:53:19,789] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0faf7580-9c7e-411f-9452-d62c653a0277/dqc_reference/checkm_data
[2023-03-15 07:53:19,790] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:53:19,804] [INFO] Task started: CheckM
[2023-03-15 07:53:19,804] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10741/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10741/checkm_input OceanDNA-b10741/checkm_result
[2023-03-15 07:54:14,492] [INFO] Task succeeded: CheckM
[2023-03-15 07:54:14,493] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.94%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 07:54:14,496] [INFO] ===== Completeness check finished =====
[2023-03-15 07:54:14,496] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:54:14,496] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10741/markers.fasta)
[2023-03-15 07:54:14,496] [INFO] Task started: Blastn
[2023-03-15 07:54:14,496] [INFO] Running command: blastn -query OceanDNA-b10741/markers.fasta -db /var/lib/cwl/stg0faf7580-9c7e-411f-9452-d62c653a0277/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10741/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:54:15,383] [INFO] Task succeeded: Blastn
[2023-03-15 07:54:15,384] [INFO] Selected 17 target genomes.
[2023-03-15 07:54:15,384] [INFO] Target genome list was writen to OceanDNA-b10741/target_genomes_gtdb.txt
[2023-03-15 07:54:15,423] [INFO] Task started: fastANI
[2023-03-15 07:54:15,424] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f9255bc-ad3d-4e9d-9642-155d60c5a47e/OceanDNA-b10741.fa --refList OceanDNA-b10741/target_genomes_gtdb.txt --output OceanDNA-b10741/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:54:27,280] [INFO] Task succeeded: fastANI
[2023-03-15 07:54:27,291] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 07:54:27,291] [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_002441545.1	s__Yeosuana sp002441545	79.22	472	1082	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Yeosuana	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011762485.1	s__Yeosuana marina	78.8605	476	1082	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	78.848	435	1082	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Yeosuana	95.0	99.75	99.57	0.88	0.85	11	-
GCF_014646655.1	s__Yeosuana aromativorans	78.2873	428	1082	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Yeosuana	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000789235.1	s__Wocania ichthyoenteri	78.017	342	1082	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114265.1	s__Flaviramulus basaltis	77.9938	384	1082	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003258355.1	s__Confluentibacter sp003258355	77.9053	357	1082	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Confluentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001310225.1	s__Algibacter_A alginicilyticus	77.6399	298	1082	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_004791695.1	s__Flavivirga rizhaonensis	77.3937	331	1082	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013151975.1	s__PRS1 sp013151975	77.2804	166	1082	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__PRS1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008084905.1	s__Xanthomarina maritima	77.2133	241	1082	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002886045.1	s__Flavivirga eckloniae	77.1409	261	1082	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610635.1	s__Ichthyenterobacterium magnum	77.0995	238	1082	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ichthyenterobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014638915.1	s__Xanthomarina arctica	77.0614	225	1082	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004310325.1	s__Jejuia sp004310325	76.8676	202	1082	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860825.1	s__Oceanihabitans sp018860825	76.8609	257	1082	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425305.1	s__Psychroserpens burtonensis	76.5223	167	1082	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	99.48	99.48	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-03-15 07:54:27,291] [INFO] GTDB search result was written to OceanDNA-b10741/result_gtdb.tsv
[2023-03-15 07:54:27,291] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:54:27,293] [INFO] DFAST_QC result json was written to OceanDNA-b10741/dqc_result.json
[2023-03-15 07:54:27,294] [INFO] DFAST_QC completed!
[2023-03-15 07:54:27,294] [INFO] Total running time: 0h1m47s