[2023-03-18 06:37:03,360] [INFO] DFAST_QC pipeline started.
[2023-03-18 06:37:03,360] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 06:37:03,360] [INFO] DQC Reference Directory: /var/lib/cwl/stga3c9d8c5-b11c-415f-9059-532140ec0cbb/dqc_reference
[2023-03-18 06:37:04,459] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 06:37:04,459] [INFO] Task started: Prodigal
[2023-03-18 06:37:04,460] [INFO] Running command: cat /var/lib/cwl/stg55436104-9f12-4047-8e0e-42d696eeeee7/OceanDNA-b10724.fa | prodigal -d OceanDNA-b10724/cds.fna -a OceanDNA-b10724/protein.faa -g 11 -q > /dev/null
[2023-03-18 06:37:28,477] [INFO] Task succeeded: Prodigal
[2023-03-18 06:37:28,477] [INFO] Task started: HMMsearch
[2023-03-18 06:37:28,477] [INFO] Running command: hmmsearch --tblout OceanDNA-b10724/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga3c9d8c5-b11c-415f-9059-532140ec0cbb/dqc_reference/reference_markers.hmm OceanDNA-b10724/protein.faa > /dev/null
[2023-03-18 06:37:28,684] [INFO] Task succeeded: HMMsearch
[2023-03-18 06:37:28,685] [INFO] Found 6/6 markers.
[2023-03-18 06:37:28,705] [INFO] Query marker FASTA was written to OceanDNA-b10724/markers.fasta
[2023-03-18 06:37:28,705] [INFO] Task started: Blastn
[2023-03-18 06:37:28,705] [INFO] Running command: blastn -query OceanDNA-b10724/markers.fasta -db /var/lib/cwl/stga3c9d8c5-b11c-415f-9059-532140ec0cbb/dqc_reference/reference_markers.fasta -out OceanDNA-b10724/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:37:29,282] [INFO] Task succeeded: Blastn
[2023-03-18 06:37:29,282] [INFO] Selected 28 target genomes.
[2023-03-18 06:37:29,283] [INFO] Target genome list was writen to OceanDNA-b10724/target_genomes.txt
[2023-03-18 06:37:29,299] [INFO] Task started: fastANI
[2023-03-18 06:37:29,299] [INFO] Running command: fastANI --query /var/lib/cwl/stg55436104-9f12-4047-8e0e-42d696eeeee7/OceanDNA-b10724.fa --refList OceanDNA-b10724/target_genomes.txt --output OceanDNA-b10724/fastani_result.tsv --threads 1
[2023-03-18 06:37:44,979] [INFO] Task succeeded: fastANI
[2023-03-18 06:37:44,979] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga3c9d8c5-b11c-415f-9059-532140ec0cbb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 06:37:44,980] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga3c9d8c5-b11c-415f-9059-532140ec0cbb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 06:37:44,997] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 06:37:44,997] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 06:37:44,997] [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
Altibacter lentus	strain=JLT2010	GCA_000746845.1	1223410	1223410	type	True	78.1688	146	1082	95	below_threshold
Marinirhabdus gelatinilytica	strain=DSM 101478	GCA_003353425.1	1703343	1703343	type	True	78.1517	339	1082	95	below_threshold
Marixanthomonas ophiurae	strain=KMM 3046	GCA_003413745.1	387659	387659	type	True	77.3712	173	1082	95	below_threshold
Aequorivita lipolytica	strain=Y10-2	GCA_007997135.1	153267	153267	type	True	77.1509	118	1082	95	below_threshold
Cochleicola gelatinilyticus	strain=LPB0005	GCA_001637325.1	1763537	1763537	type	True	76.863	160	1082	95	below_threshold
Ulvibacter antarcticus	strain=DSM 23424	GCA_003688405.1	442714	442714	type	True	76.7677	120	1082	95	below_threshold
Ulvibacter litoralis	strain=DSM 16195	GCA_900102055.1	227084	227084	type	True	76.7545	173	1082	95	below_threshold
Ulvibacter litoralis	strain=KCTC 12104	GCA_014651275.1	227084	227084	type	True	76.6918	174	1082	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	76.6885	60	1082	95	below_threshold
Aequorivita soesokkakensis	strain=RSSK-12	GCA_001641085.1	1385699	1385699	type	True	76.666	117	1082	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	76.6238	54	1082	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	76.5861	57	1082	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.5302	68	1082	95	below_threshold
Marixanthomonas spongiae	strain=HN-E44	GCA_003095375.1	2174845	2174845	type	True	76.5229	129	1082	95	below_threshold
Changchengzhania lutea	strain=SM1355	GCA_006974145.1	2049305	2049305	type	True	76.489	50	1082	95	below_threshold
Aequorivita sublithincola	strain=DSM 14238	GCA_000265385.1	101385	101385	type	True	76.4761	108	1082	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	76.4696	68	1082	95	below_threshold
Mariniflexile gromovii	strain=KCTC 12570	GCA_017814435.1	362523	362523	type	True	76.3212	65	1082	95	below_threshold
Aestuariivivens insulae	strain=AH-MY3	GCA_022662195.1	1621988	1621988	type	True	76.2573	63	1082	95	below_threshold
Aestuariibaculum marinum	strain=IP7	GCA_014596975.1	2683592	2683592	type	True	76.2572	60	1082	95	below_threshold
Aequorivita echinoideorum	strain=JCM30378	GCA_018476645.1	1549647	1549647	type	True	76.1747	106	1082	95	below_threshold
Hyunsoonleella aquatilis	strain=SJ7	GCA_014270105.1	2762758	2762758	type	True	75.9071	62	1082	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	75.9037	63	1082	95	below_threshold
Aquimarina muelleri	strain=DSM 19832	GCA_000430665.1	279356	279356	type	True	75.7202	52	1082	95	below_threshold
Aquimarina muelleri	strain=KCTC 12285	GCA_014651355.1	279356	279356	type	True	75.6957	51	1082	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 06:37:44,997] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10724/tc_result.tsv
[2023-03-18 06:37:44,997] [INFO] ===== Taxonomy check completed =====
[2023-03-18 06:37:44,997] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 06:37:44,998] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga3c9d8c5-b11c-415f-9059-532140ec0cbb/dqc_reference/checkm_data
[2023-03-18 06:37:44,998] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 06:37:45,003] [INFO] Task started: CheckM
[2023-03-18 06:37:45,003] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10724/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10724/checkm_input OceanDNA-b10724/checkm_result
[2023-03-18 06:38:44,716] [INFO] Task succeeded: CheckM
[2023-03-18 06:38:44,716] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 06:38:44,719] [INFO] ===== Completeness check finished =====
[2023-03-18 06:38:44,719] [INFO] ===== Start GTDB Search =====
[2023-03-18 06:38:44,719] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10724/markers.fasta)
[2023-03-18 06:38:44,720] [INFO] Task started: Blastn
[2023-03-18 06:38:44,720] [INFO] Running command: blastn -query OceanDNA-b10724/markers.fasta -db /var/lib/cwl/stga3c9d8c5-b11c-415f-9059-532140ec0cbb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10724/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:38:45,519] [INFO] Task succeeded: Blastn
[2023-03-18 06:38:45,520] [INFO] Selected 18 target genomes.
[2023-03-18 06:38:45,520] [INFO] Target genome list was writen to OceanDNA-b10724/target_genomes_gtdb.txt
[2023-03-18 06:38:45,741] [INFO] Task started: fastANI
[2023-03-18 06:38:45,741] [INFO] Running command: fastANI --query /var/lib/cwl/stg55436104-9f12-4047-8e0e-42d696eeeee7/OceanDNA-b10724.fa --refList OceanDNA-b10724/target_genomes_gtdb.txt --output OceanDNA-b10724/fastani_result_gtdb.tsv --threads 1
[2023-03-18 06:38:55,307] [INFO] Task succeeded: fastANI
[2023-03-18 06:38:55,316] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 06:38:55,316] [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_002375495.1	s__Marinirhabdus sp002375495	98.3855	1021	1082	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	98.31	97.88	0.90	0.71	8	conclusive
GCA_002337605.1	s__Marinirhabdus sp002337605	78.9005	354	1082	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	98.69	98.69	0.95	0.95	2	-
GCA_011044175.1	s__Marinirhabdus sp011044175	78.4578	412	1082	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002707745.1	s__Marinirhabdus sp002707745	78.4076	270	1082	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	99.79	99.79	0.83	0.83	2	-
GCF_003353425.1	s__Marinirhabdus gelatinilytica	78.1423	340	1082	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003413745.1	s__Marixanthomonas ophiurae	77.3559	174	1082	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900489465.1	s__Aequorivita sp900489465	76.9984	116	1082	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001637325.1	s__Cochleicola gelatinilyticus	76.865	160	1082	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cochleicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003688405.1	s__Ulvibacter antarcticus	76.7677	120	1082	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ulvibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102055.1	s__Ulvibacter litoralis	76.7563	173	1082	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ulvibacter	95.0	99.98	99.98	1.00	1.00	2	-
GCA_009827225.1	s__SMXJ01 sp009827225	76.6047	88	1082	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SMXJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001573155.1	s__Aequorivita aquimaris	76.6016	129	1082	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003095375.1	s__Marixanthomonas sp003095375	76.5229	129	1082	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002707025.1	s__IN17 sp002707025	76.5217	124	1082	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__IN17	95.0	99.83	99.78	0.96	0.93	3	-
GCA_013043685.1	s__Pukyongia sp013043685	76.3023	80	1082	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pukyongia	95.0	99.85	99.75	0.96	0.95	6	-
GCF_018476645.1	s__Aequorivita echinoideorum	76.1607	107	1082	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 06:38:55,316] [INFO] GTDB search result was written to OceanDNA-b10724/result_gtdb.tsv
[2023-03-18 06:38:55,317] [INFO] ===== GTDB Search completed =====
[2023-03-18 06:38:55,319] [INFO] DFAST_QC result json was written to OceanDNA-b10724/dqc_result.json
[2023-03-18 06:38:55,319] [INFO] DFAST_QC completed!
[2023-03-18 06:38:55,319] [INFO] Total running time: 0h1m52s