[2023-03-16 10:20:34,584] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:20:34,584] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:20:34,584] [INFO] DQC Reference Directory: /var/lib/cwl/stgdd9269de-db79-4021-9ebd-258be09cf8a1/dqc_reference
[2023-03-16 10:20:35,837] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:20:35,837] [INFO] Task started: Prodigal
[2023-03-16 10:20:35,838] [INFO] Running command: cat /var/lib/cwl/stg54588568-0dc8-478b-90d9-3df63645556c/OceanDNA-b7333.fa | prodigal -d OceanDNA-b7333/cds.fna -a OceanDNA-b7333/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:20:50,418] [INFO] Task succeeded: Prodigal
[2023-03-16 10:20:50,419] [INFO] Task started: HMMsearch
[2023-03-16 10:20:50,419] [INFO] Running command: hmmsearch --tblout OceanDNA-b7333/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdd9269de-db79-4021-9ebd-258be09cf8a1/dqc_reference/reference_markers.hmm OceanDNA-b7333/protein.faa > /dev/null
[2023-03-16 10:20:50,644] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:20:50,644] [INFO] Found 6/6 markers.
[2023-03-16 10:20:50,661] [INFO] Query marker FASTA was written to OceanDNA-b7333/markers.fasta
[2023-03-16 10:20:50,661] [INFO] Task started: Blastn
[2023-03-16 10:20:50,662] [INFO] Running command: blastn -query OceanDNA-b7333/markers.fasta -db /var/lib/cwl/stgdd9269de-db79-4021-9ebd-258be09cf8a1/dqc_reference/reference_markers.fasta -out OceanDNA-b7333/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:20:51,275] [INFO] Task succeeded: Blastn
[2023-03-16 10:20:51,276] [INFO] Selected 31 target genomes.
[2023-03-16 10:20:51,276] [INFO] Target genome list was writen to OceanDNA-b7333/target_genomes.txt
[2023-03-16 10:20:51,340] [INFO] Task started: fastANI
[2023-03-16 10:20:51,340] [INFO] Running command: fastANI --query /var/lib/cwl/stg54588568-0dc8-478b-90d9-3df63645556c/OceanDNA-b7333.fa --refList OceanDNA-b7333/target_genomes.txt --output OceanDNA-b7333/fastani_result.tsv --threads 1
[2023-03-16 10:21:10,248] [INFO] Task succeeded: fastANI
[2023-03-16 10:21:10,249] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdd9269de-db79-4021-9ebd-258be09cf8a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:21:10,249] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdd9269de-db79-4021-9ebd-258be09cf8a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:21:10,264] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:21:10,264] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 10:21:10,264] [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	76.5756	100	688	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	76.3754	85	688	95	below_threshold
Winogradskyella psychrotolerans	strain=RS-3	GCA_000427335.1	1344585	1344585	type	True	76.3559	88	688	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	76.2913	63	688	95	below_threshold
Winogradskyella helgolandensis	strain=Z963	GCA_013404085.1	2697010	2697010	type	True	76.2909	91	688	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	76.2637	72	688	95	below_threshold
Winogradskyella undariae	strain=CCUG 63832	GCA_013285155.1	1285465	1285465	type	True	76.2634	87	688	95	below_threshold
Confluentibacter sediminis	strain=DSL-48	GCA_003258355.1	2219045	2219045	type	True	76.2313	65	688	95	below_threshold
Changchengzhania lutea	strain=SM1355	GCA_006974145.1	2049305	2049305	type	True	76.2285	88	688	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	76.2093	86	688	95	below_threshold
Bizionia algoritergicola	strain=APA-1	GCA_008086165.1	291187	291187	type	True	76.204	94	688	95	below_threshold
Mesoflavibacter zeaxanthinifaciens subsp. sabulilitoris	strain=CECT 8597	GCA_014191595.1	1520893	393060	type	True	76.1512	71	688	95	below_threshold
Mesoflavibacter zeaxanthinifaciens subsp. sabulilitoris	strain=KCTC 42117	GCA_003008435.1	1520893	393060	type	True	76.127	72	688	95	below_threshold
Algibacter pectinivorans	strain=DSM 25730	GCA_900112595.1	870482	870482	type	True	76.1129	75	688	95	below_threshold
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	76.1082	92	688	95	below_threshold
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	76.0798	89	688	95	below_threshold
Olleya aquimaris	strain=DSM 24464	GCA_003259525.1	639310	639310	type	True	76.0773	83	688	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	76.0205	86	688	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	76.0045	65	688	95	below_threshold
Winogradskyella wichelsiae	strain=Z738	GCA_013403925.1	2697007	2697007	type	True	75.9689	82	688	95	below_threshold
Mariniflexile gromovii	strain=KCTC 12570	GCA_017814435.1	362523	362523	type	True	75.9639	76	688	95	below_threshold
Algibacter alginicilyticus	strain=HZ22	GCA_001310225.1	1736674	1736674	type	True	75.8703	81	688	95	below_threshold
Winogradskyella eckloniae	strain=EC29	GCA_013249045.1	1089306	1089306	type	True	75.8568	87	688	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	75.7644	69	688	95	below_threshold
Gelidibacter gilvus	strain=IC158	GCA_004115975.1	59602	59602	type	True	75.7309	74	688	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	75.6939	57	688	95	below_threshold
Winogradskyella ursingii	strain=HL4150	GCA_013403975.1	2686079	2686079	type	True	75.5322	59	688	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 10:21:10,265] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7333/tc_result.tsv
[2023-03-16 10:21:10,265] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:21:10,265] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:21:10,265] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdd9269de-db79-4021-9ebd-258be09cf8a1/dqc_reference/checkm_data
[2023-03-16 10:21:10,266] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:21:10,271] [INFO] Task started: CheckM
[2023-03-16 10:21:10,271] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7333/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7333/checkm_input OceanDNA-b7333/checkm_result
[2023-03-16 10:21:53,065] [INFO] Task succeeded: CheckM
[2023-03-16 10:21:53,066] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.75%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 10:21:53,068] [INFO] ===== Completeness check finished =====
[2023-03-16 10:21:53,069] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:21:53,069] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7333/markers.fasta)
[2023-03-16 10:21:53,069] [INFO] Task started: Blastn
[2023-03-16 10:21:53,070] [INFO] Running command: blastn -query OceanDNA-b7333/markers.fasta -db /var/lib/cwl/stgdd9269de-db79-4021-9ebd-258be09cf8a1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7333/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:21:53,891] [INFO] Task succeeded: Blastn
[2023-03-16 10:21:53,893] [INFO] Selected 9 target genomes.
[2023-03-16 10:21:53,893] [INFO] Target genome list was writen to OceanDNA-b7333/target_genomes_gtdb.txt
[2023-03-16 10:21:53,900] [INFO] Task started: fastANI
[2023-03-16 10:21:53,900] [INFO] Running command: fastANI --query /var/lib/cwl/stg54588568-0dc8-478b-90d9-3df63645556c/OceanDNA-b7333.fa --refList OceanDNA-b7333/target_genomes_gtdb.txt --output OceanDNA-b7333/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:21:58,043] [INFO] Task succeeded: fastANI
[2023-03-16 10:21:58,050] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 10:21:58,050] [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_001735745.1	s__Hel1-33-131 sp001735745	92.2136	621	688	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	85.0373	534	688	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	84.1853	495	688	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_018608725.1	s__Hel1-33-131 sp018608725	84.1244	435	688	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	82.1104	362	688	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	81.6512	430	688	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	79.1325	255	688	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	78.7627	276	688	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	-
GCA_018608705.1	s__Hel1-33-131 sp018608705	78.2698	186	688	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	99.44	99.44	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-03-16 10:21:58,051] [INFO] GTDB search result was written to OceanDNA-b7333/result_gtdb.tsv
[2023-03-16 10:21:58,051] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:21:58,053] [INFO] DFAST_QC result json was written to OceanDNA-b7333/dqc_result.json
[2023-03-16 10:21:58,053] [INFO] DFAST_QC completed!
[2023-03-16 10:21:58,053] [INFO] Total running time: 0h1m23s