[2023-03-14 10:55:58,922] [INFO] DFAST_QC pipeline started.
[2023-03-14 10:55:58,922] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 10:55:58,922] [INFO] DQC Reference Directory: /var/lib/cwl/stga56e1c9a-1e87-486d-a0d5-42a21f68b7cd/dqc_reference
[2023-03-14 10:56:00,679] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 10:56:00,679] [INFO] Task started: Prodigal
[2023-03-14 10:56:00,680] [INFO] Running command: cat /var/lib/cwl/stge79b2cae-f299-4c32-935f-906b254ab108/OceanDNA-b7023.fa | prodigal -d OceanDNA-b7023/cds.fna -a OceanDNA-b7023/protein.faa -g 11 -q > /dev/null
[2023-03-14 10:56:13,679] [INFO] Task succeeded: Prodigal
[2023-03-14 10:56:13,679] [INFO] Task started: HMMsearch
[2023-03-14 10:56:13,679] [INFO] Running command: hmmsearch --tblout OceanDNA-b7023/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga56e1c9a-1e87-486d-a0d5-42a21f68b7cd/dqc_reference/reference_markers.hmm OceanDNA-b7023/protein.faa > /dev/null
[2023-03-14 10:56:13,903] [INFO] Task succeeded: HMMsearch
[2023-03-14 10:56:13,904] [INFO] Found 6/6 markers.
[2023-03-14 10:56:13,921] [INFO] Query marker FASTA was written to OceanDNA-b7023/markers.fasta
[2023-03-14 10:56:13,921] [INFO] Task started: Blastn
[2023-03-14 10:56:13,921] [INFO] Running command: blastn -query OceanDNA-b7023/markers.fasta -db /var/lib/cwl/stga56e1c9a-1e87-486d-a0d5-42a21f68b7cd/dqc_reference/reference_markers.fasta -out OceanDNA-b7023/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:56:14,538] [INFO] Task succeeded: Blastn
[2023-03-14 10:56:14,539] [INFO] Selected 32 target genomes.
[2023-03-14 10:56:14,539] [INFO] Target genome list was writen to OceanDNA-b7023/target_genomes.txt
[2023-03-14 10:56:14,550] [INFO] Task started: fastANI
[2023-03-14 10:56:14,550] [INFO] Running command: fastANI --query /var/lib/cwl/stge79b2cae-f299-4c32-935f-906b254ab108/OceanDNA-b7023.fa --refList OceanDNA-b7023/target_genomes.txt --output OceanDNA-b7023/fastani_result.tsv --threads 1
[2023-03-14 10:56:33,207] [INFO] Task succeeded: fastANI
[2023-03-14 10:56:33,208] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga56e1c9a-1e87-486d-a0d5-42a21f68b7cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 10:56:33,208] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga56e1c9a-1e87-486d-a0d5-42a21f68b7cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 10:56:33,224] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 10:56:33,224] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 10:56:33,224] [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
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	76.7876	121	686	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	76.7236	98	686	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	76.7236	98	686	95	below_threshold
Bizionia algoritergicola	strain=APA-1	GCA_008086165.1	291187	291187	type	True	76.7012	83	686	95	below_threshold
Winogradskyella helgolandensis	strain=Z963	GCA_013404085.1	2697010	2697010	type	True	76.6637	101	686	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	76.4882	86	686	95	below_threshold
Winogradskyella thalassocola	strain=DSM 15363	GCA_900099995.1	262004	262004	type	True	76.4578	102	686	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.447	87	686	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	76.4278	118	686	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	76.4071	74	686	95	below_threshold
Aquimarina amphilecti	strain=DSM 25232	GCA_900109375.1	1038014	1038014	type	True	76.3781	94	686	95	below_threshold
Aequorivita sinensis	strain=S1-10	GCA_006346335.1	1382458	1382458	type	True	76.3702	95	686	95	below_threshold
Aequorivita lipolytica	strain=Y10-2	GCA_007997135.1	153267	153267	type	True	76.3487	81	686	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	76.3442	85	686	95	below_threshold
Psychroserpens mesophilus	strain=JCM 13413	GCA_000826645.1	325473	325473	type	True	76.2921	100	686	95	below_threshold
Winogradskyella wichelsiae	strain=Z738	GCA_013403925.1	2697007	2697007	type	True	76.2742	109	686	95	below_threshold
Cellulophaga tyrosinoxydans	strain=DSM 21164	GCA_900176415.1	504486	504486	type	True	76.264	72	686	95	below_threshold
Confluentibacter sediminis	strain=DSL-48	GCA_003258355.1	2219045	2219045	type	True	76.2603	94	686	95	below_threshold
Cochleicola gelatinilyticus	strain=LPB0005	GCA_001637325.1	1763537	1763537	type	True	76.2216	123	686	95	below_threshold
Aquimarina muelleri	strain=DSM 19832	GCA_000430665.1	279356	279356	type	True	76.1504	93	686	95	below_threshold
Winogradskyella undariae	strain=CCUG 63832	GCA_013285155.1	1285465	1285465	type	True	76.129	112	686	95	below_threshold
Aquimarina muelleri	strain=KCTC 12285	GCA_014651355.1	279356	279356	type	True	76.1065	93	686	95	below_threshold
Aequorivita antarctica	strain=SW49	GCA_007997155.1	153266	153266	type	True	76.0691	73	686	95	below_threshold
Bizionia echini	strain=DSM 23925	GCA_900115185.1	649333	649333	type	True	76.0442	92	686	95	below_threshold
Aequorivita aquimaris	strain=D-24	GCA_001573155.1	1548749	1548749	type	True	75.9215	61	686	95	below_threshold
Mesonia hippocampi	strain=DSM 29568	GCA_014197445.1	1628250	1628250	type	True	75.8959	59	686	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	75.8814	90	686	95	below_threshold
Winogradskyella jejuensis	strain=DSM 25330	GCA_900129745.1	1089305	1089305	type	True	75.8362	71	686	95	below_threshold
Cellulophaga algicola	strain=DSM 14237	GCA_000186265.1	59600	59600	type	True	75.8153	93	686	95	below_threshold
Flavobacterium jumunjinense	strain=HME7102	GCA_021650975.2	998845	998845	type	True	75.7671	78	686	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 10:56:33,224] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7023/tc_result.tsv
[2023-03-14 10:56:33,224] [INFO] ===== Taxonomy check completed =====
[2023-03-14 10:56:33,224] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 10:56:33,225] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga56e1c9a-1e87-486d-a0d5-42a21f68b7cd/dqc_reference/checkm_data
[2023-03-14 10:56:33,225] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 10:56:33,315] [INFO] Task started: CheckM
[2023-03-14 10:56:33,315] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7023/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7023/checkm_input OceanDNA-b7023/checkm_result
[2023-03-14 10:57:08,159] [INFO] Task succeeded: CheckM
[2023-03-14 10:57:08,159] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.89%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 10:57:08,161] [INFO] ===== Completeness check finished =====
[2023-03-14 10:57:08,161] [INFO] ===== Start GTDB Search =====
[2023-03-14 10:57:08,162] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7023/markers.fasta)
[2023-03-14 10:57:08,162] [INFO] Task started: Blastn
[2023-03-14 10:57:08,162] [INFO] Running command: blastn -query OceanDNA-b7023/markers.fasta -db /var/lib/cwl/stga56e1c9a-1e87-486d-a0d5-42a21f68b7cd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7023/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:57:09,016] [INFO] Task succeeded: Blastn
[2023-03-14 10:57:09,017] [INFO] Selected 9 target genomes.
[2023-03-14 10:57:09,017] [INFO] Target genome list was writen to OceanDNA-b7023/target_genomes_gtdb.txt
[2023-03-14 10:57:09,050] [INFO] Task started: fastANI
[2023-03-14 10:57:09,050] [INFO] Running command: fastANI --query /var/lib/cwl/stge79b2cae-f299-4c32-935f-906b254ab108/OceanDNA-b7023.fa --refList OceanDNA-b7023/target_genomes_gtdb.txt --output OceanDNA-b7023/fastani_result_gtdb.tsv --threads 1
[2023-03-14 10:57:13,295] [INFO] Task succeeded: fastANI
[2023-03-14 10:57:13,301] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 10:57:13,301] [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_018669795.1	s__GCA-002733185 sp018669795	93.1134	595	686	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	98.54	95.82	0.94	0.91	4	-
GCA_002713705.1	s__GCA-002733185 sp002713705	89.5888	598	686	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	97.32	97.11	0.93	0.92	3	-
GCA_905181835.1	s__GCA-002733185 sp905181835	79.1553	322	686	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733185.1	s__GCA-002733185 sp002733185	78.8151	292	686	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004213605.1	s__GCA-002733185 sp004213605	78.4517	214	686	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	95.79	95.79	0.89	0.89	2	-
GCA_004214175.1	s__GCA-002733185 sp004214175	78.3599	201	686	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002733185	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011762485.1	s__Yeosuana marina	76.4426	99	686	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Yeosuana	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001637325.1	s__Cochleicola gelatinilyticus	76.2085	124	686	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cochleicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 10:57:13,301] [INFO] GTDB search result was written to OceanDNA-b7023/result_gtdb.tsv
[2023-03-14 10:57:13,301] [INFO] ===== GTDB Search completed =====
[2023-03-14 10:57:13,303] [INFO] DFAST_QC result json was written to OceanDNA-b7023/dqc_result.json
[2023-03-14 10:57:13,304] [INFO] DFAST_QC completed!
[2023-03-14 10:57:13,304] [INFO] Total running time: 0h1m14s