[2023-03-15 12:44:24,469] [INFO] DFAST_QC pipeline started.
[2023-03-15 12:44:24,470] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 12:44:24,470] [INFO] DQC Reference Directory: /var/lib/cwl/stg3afca1ff-ec71-4800-9b42-690cd33b34d2/dqc_reference
[2023-03-15 12:44:26,207] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 12:44:26,207] [INFO] Task started: Prodigal
[2023-03-15 12:44:26,208] [INFO] Running command: cat /var/lib/cwl/stg8cd5fe71-e2fb-4837-87e7-9671076e989b/OceanDNA-b10747.fa | prodigal -d OceanDNA-b10747/cds.fna -a OceanDNA-b10747/protein.faa -g 11 -q > /dev/null
[2023-03-15 12:44:45,380] [INFO] Task succeeded: Prodigal
[2023-03-15 12:44:45,381] [INFO] Task started: HMMsearch
[2023-03-15 12:44:45,381] [INFO] Running command: hmmsearch --tblout OceanDNA-b10747/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3afca1ff-ec71-4800-9b42-690cd33b34d2/dqc_reference/reference_markers.hmm OceanDNA-b10747/protein.faa > /dev/null
[2023-03-15 12:44:45,642] [INFO] Task succeeded: HMMsearch
[2023-03-15 12:44:45,642] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8cd5fe71-e2fb-4837-87e7-9671076e989b/OceanDNA-b10747.fa]
[2023-03-15 12:44:45,663] [INFO] Query marker FASTA was written to OceanDNA-b10747/markers.fasta
[2023-03-15 12:44:45,664] [INFO] Task started: Blastn
[2023-03-15 12:44:45,664] [INFO] Running command: blastn -query OceanDNA-b10747/markers.fasta -db /var/lib/cwl/stg3afca1ff-ec71-4800-9b42-690cd33b34d2/dqc_reference/reference_markers.fasta -out OceanDNA-b10747/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:44:46,258] [INFO] Task succeeded: Blastn
[2023-03-15 12:44:46,259] [INFO] Selected 19 target genomes.
[2023-03-15 12:44:46,259] [INFO] Target genome list was writen to OceanDNA-b10747/target_genomes.txt
[2023-03-15 12:44:46,270] [INFO] Task started: fastANI
[2023-03-15 12:44:46,270] [INFO] Running command: fastANI --query /var/lib/cwl/stg8cd5fe71-e2fb-4837-87e7-9671076e989b/OceanDNA-b10747.fa --refList OceanDNA-b10747/target_genomes.txt --output OceanDNA-b10747/fastani_result.tsv --threads 1
[2023-03-15 12:45:00,199] [INFO] Task succeeded: fastANI
[2023-03-15 12:45:00,200] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3afca1ff-ec71-4800-9b42-690cd33b34d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 12:45:00,200] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3afca1ff-ec71-4800-9b42-690cd33b34d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 12:45:00,211] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 12:45:00,211] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 12:45:00,211] [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	79.1632	531	954	95	below_threshold
Yeosuana aromativorans	strain=JCM 12862	GCA_014646655.1	288019	288019	type	True	79.1137	425	954	95	below_threshold
Confluentibacter sediminis	strain=DSL-48	GCA_003258355.1	2219045	2219045	type	True	78.0286	283	954	95	below_threshold
Confluentibacter flavum	strain=3B	GCA_002843175.1	1909700	1909700	type	True	77.8037	307	954	95	below_threshold
Mariniflexile gromovii	strain=KCTC 12570	GCA_017814435.1	362523	362523	type	True	77.7875	291	954	95	below_threshold
Mariniflexile fucanivorans	strain=DSM 18792	GCA_004341235.1	264023	264023	type	True	77.7871	298	954	95	below_threshold
Changchengzhania lutea	strain=SM1355	GCA_006974145.1	2049305	2049305	type	True	77.6596	283	954	95	below_threshold
Confluentibacter lentus	strain=HJM-3	GCA_002806995.1	1699412	1699412	type	True	77.6184	256	954	95	below_threshold
Algibacter alginicilyticus	strain=HZ22	GCA_001310225.1	1736674	1736674	type	True	77.6069	271	954	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	77.5763	260	954	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	77.4275	252	954	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	77.341	192	954	95	below_threshold
Flavivirga eckloniae	strain=ECD14	GCA_002886045.1	1803846	1803846	type	True	77.3107	240	954	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	77.2411	166	954	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	77.1379	147	954	95	below_threshold
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	76.916	199	954	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	76.8126	164	954	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	76.7893	178	954	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	76.5716	151	954	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 12:45:00,211] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10747/tc_result.tsv
[2023-03-15 12:45:00,211] [INFO] ===== Taxonomy check completed =====
[2023-03-15 12:45:00,212] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 12:45:00,212] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3afca1ff-ec71-4800-9b42-690cd33b34d2/dqc_reference/checkm_data
[2023-03-15 12:45:00,212] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 12:45:00,229] [INFO] Task started: CheckM
[2023-03-15 12:45:00,230] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10747/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10747/checkm_input OceanDNA-b10747/checkm_result
[2023-03-15 12:45:49,699] [INFO] Task succeeded: CheckM
[2023-03-15 12:45:49,699] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.46%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 12:45:49,702] [INFO] ===== Completeness check finished =====
[2023-03-15 12:45:49,702] [INFO] ===== Start GTDB Search =====
[2023-03-15 12:45:49,702] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10747/markers.fasta)
[2023-03-15 12:45:49,703] [INFO] Task started: Blastn
[2023-03-15 12:45:49,704] [INFO] Running command: blastn -query OceanDNA-b10747/markers.fasta -db /var/lib/cwl/stg3afca1ff-ec71-4800-9b42-690cd33b34d2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10747/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:45:50,505] [INFO] Task succeeded: Blastn
[2023-03-15 12:45:50,506] [INFO] Selected 16 target genomes.
[2023-03-15 12:45:50,506] [INFO] Target genome list was writen to OceanDNA-b10747/target_genomes_gtdb.txt
[2023-03-15 12:45:50,576] [INFO] Task started: fastANI
[2023-03-15 12:45:50,576] [INFO] Running command: fastANI --query /var/lib/cwl/stg8cd5fe71-e2fb-4837-87e7-9671076e989b/OceanDNA-b10747.fa --refList OceanDNA-b10747/target_genomes_gtdb.txt --output OceanDNA-b10747/fastani_result_gtdb.tsv --threads 1
[2023-03-15 12:46:02,325] [INFO] Task succeeded: fastANI
[2023-03-15 12:46:02,334] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 12:46:02,334] [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	79.1543	532	954	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Yeosuana	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646655.1	s__Yeosuana aromativorans	79.1148	424	954	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	78.8322	435	954	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	78.5939	371	954	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	78.1019	293	954	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	77.9255	344	954	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002843175.1	s__Confluentibacter flavum	77.8142	306	954	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Confluentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003425985.1	s__Mariniflexile sp002848895	77.7433	313	954	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mariniflexile	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001747085.1	s__Algibacter_C aquaticus	77.6615	238	954	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001310225.1	s__Algibacter_A alginicilyticus	77.6306	269	954	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	77.5342	263	954	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143755.1	s__Algibacter_B sp003143755	77.4253	253	954	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002886045.1	s__Flavivirga eckloniae	77.3081	241	954	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	77.2537	192	954	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ichthyenterobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004310325.1	s__Jejuia sp004310325	76.7899	179	954	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015319355.1	s__Psychroserpens luteus	76.5313	172	954	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 12:46:02,335] [INFO] GTDB search result was written to OceanDNA-b10747/result_gtdb.tsv
[2023-03-15 12:46:02,335] [INFO] ===== GTDB Search completed =====
[2023-03-15 12:46:02,337] [INFO] DFAST_QC result json was written to OceanDNA-b10747/dqc_result.json
[2023-03-15 12:46:02,337] [INFO] DFAST_QC completed!
[2023-03-15 12:46:02,337] [INFO] Total running time: 0h1m38s