[2023-03-16 00:13:32,253] [INFO] DFAST_QC pipeline started.
[2023-03-16 00:13:32,253] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 00:13:32,253] [INFO] DQC Reference Directory: /var/lib/cwl/stg55cbc093-ba5e-4456-9fe2-89e6d93c5444/dqc_reference
[2023-03-16 00:13:33,514] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 00:13:33,514] [INFO] Task started: Prodigal
[2023-03-16 00:13:33,514] [INFO] Running command: cat /var/lib/cwl/stgf04169a6-769f-457a-976b-4a81e56aa0a6/OceanDNA-b38974.fa | prodigal -d OceanDNA-b38974/cds.fna -a OceanDNA-b38974/protein.faa -g 11 -q > /dev/null
[2023-03-16 00:13:50,280] [INFO] Task succeeded: Prodigal
[2023-03-16 00:13:50,281] [INFO] Task started: HMMsearch
[2023-03-16 00:13:50,281] [INFO] Running command: hmmsearch --tblout OceanDNA-b38974/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg55cbc093-ba5e-4456-9fe2-89e6d93c5444/dqc_reference/reference_markers.hmm OceanDNA-b38974/protein.faa > /dev/null
[2023-03-16 00:13:50,486] [INFO] Task succeeded: HMMsearch
[2023-03-16 00:13:50,486] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf04169a6-769f-457a-976b-4a81e56aa0a6/OceanDNA-b38974.fa]
[2023-03-16 00:13:50,515] [INFO] Query marker FASTA was written to OceanDNA-b38974/markers.fasta
[2023-03-16 00:13:50,515] [INFO] Task started: Blastn
[2023-03-16 00:13:50,515] [INFO] Running command: blastn -query OceanDNA-b38974/markers.fasta -db /var/lib/cwl/stg55cbc093-ba5e-4456-9fe2-89e6d93c5444/dqc_reference/reference_markers.fasta -out OceanDNA-b38974/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:13:51,211] [INFO] Task succeeded: Blastn
[2023-03-16 00:13:51,216] [INFO] Selected 20 target genomes.
[2023-03-16 00:13:51,216] [INFO] Target genome list was writen to OceanDNA-b38974/target_genomes.txt
[2023-03-16 00:13:51,230] [INFO] Task started: fastANI
[2023-03-16 00:13:51,230] [INFO] Running command: fastANI --query /var/lib/cwl/stgf04169a6-769f-457a-976b-4a81e56aa0a6/OceanDNA-b38974.fa --refList OceanDNA-b38974/target_genomes.txt --output OceanDNA-b38974/fastani_result.tsv --threads 1
[2023-03-16 00:14:05,936] [INFO] Task succeeded: fastANI
[2023-03-16 00:14:05,936] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg55cbc093-ba5e-4456-9fe2-89e6d93c5444/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 00:14:05,936] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg55cbc093-ba5e-4456-9fe2-89e6d93c5444/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 00:14:05,947] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 00:14:05,948] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 00:14:05,948] [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
Marinobacter persicus	strain=KCTC 23561	GCA_014652295.1	930118	930118	type	True	80.9661	531	894	95	below_threshold
Marinobacter persicus	strain=IBRC-M 10445	GCA_900114155.1	930118	930118	type	True	80.904	532	894	95	below_threshold
Marinobacter vinifirmus	strain=FB1	GCA_002258215.1	355591	355591	type	True	79.8121	419	894	95	below_threshold
Marinobacter oulmenensis	strain=DSM 22359	GCA_014201735.1	643747	643747	type	True	79.3538	427	894	95	below_threshold
Marinobacter shengliensis subsp. alexandrii	strain=LZ-6	GCA_005871095.1	2570350	1389223	type	True	79.248	399	894	95	below_threshold
Marinobacter halophilus	strain=JCM 30472	GCA_003007685.1	1323740	1323740	type	True	79.0383	400	894	95	below_threshold
Marinobacter pelagius	strain=CGMCC 1.6775	GCA_900114925.1	379482	379482	type	True	78.9614	362	894	95	below_threshold
Marinobacter gudaonensis	strain=CGMCC 1.6294	GCA_900115175.1	375760	375760	type	True	78.8067	352	894	95	below_threshold
Marinobacter guineae	strain=M3B	GCA_002744735.1	432303	432303	type	True	78.7625	371	894	95	below_threshold
Marinobacter subterrani	strain=JG233	GCA_001045555.1	1658765	1658765	type	True	78.7116	375	894	95	below_threshold
Marinobacter arenosus	strain=CAU 1620	GCA_019264345.1	2856822	2856822	type	True	78.5868	313	894	95	below_threshold
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	78.5159	307	894	95	below_threshold
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	78.5021	300	894	95	below_threshold
Marinobacter santoriniensis	strain=NKSG1	GCA_000347775.1	523742	523742	type	True	78.4804	299	894	95	below_threshold
Marinobacter daepoensis	strain=DSM 16072	GCA_000421165.1	262077	262077	type	True	78.4405	321	894	95	below_threshold
Marinobacter koreensis	strain=DSM 17924	GCA_023156285.1	335974	335974	type	True	78.3839	296	894	95	below_threshold
Marinobacter halotolerans	strain=NBRC 110910	GCA_008795985.1	1569211	1569211	type	True	78.1849	273	894	95	below_threshold
Marinobacter xestospongiae	strain=JCM 17469	GCA_023156385.1	994319	994319	type	True	77.6372	259	894	95	below_threshold
Marinobacter mobilis	strain=CGMCC 1.7059	GCA_900106945.1	488533	488533	type	True	77.3951	203	894	95	below_threshold
Marinobacter changyiensis	strain=CLL7-20	GCA_009193265.1	2604091	2604091	type	True	77.0556	190	894	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 00:14:05,949] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38974/tc_result.tsv
[2023-03-16 00:14:05,950] [INFO] ===== Taxonomy check completed =====
[2023-03-16 00:14:05,950] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 00:14:05,950] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg55cbc093-ba5e-4456-9fe2-89e6d93c5444/dqc_reference/checkm_data
[2023-03-16 00:14:05,951] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 00:14:05,957] [INFO] Task started: CheckM
[2023-03-16 00:14:05,957] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38974/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38974/checkm_input OceanDNA-b38974/checkm_result
[2023-03-16 00:14:49,622] [INFO] Task succeeded: CheckM
[2023-03-16 00:14:49,622] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 00:14:49,637] [INFO] ===== Completeness check finished =====
[2023-03-16 00:14:49,637] [INFO] ===== Start GTDB Search =====
[2023-03-16 00:14:49,637] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38974/markers.fasta)
[2023-03-16 00:14:49,638] [INFO] Task started: Blastn
[2023-03-16 00:14:49,638] [INFO] Running command: blastn -query OceanDNA-b38974/markers.fasta -db /var/lib/cwl/stg55cbc093-ba5e-4456-9fe2-89e6d93c5444/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38974/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:14:50,845] [INFO] Task succeeded: Blastn
[2023-03-16 00:14:50,849] [INFO] Selected 18 target genomes.
[2023-03-16 00:14:50,849] [INFO] Target genome list was writen to OceanDNA-b38974/target_genomes_gtdb.txt
[2023-03-16 00:14:50,864] [INFO] Task started: fastANI
[2023-03-16 00:14:50,865] [INFO] Running command: fastANI --query /var/lib/cwl/stgf04169a6-769f-457a-976b-4a81e56aa0a6/OceanDNA-b38974.fa --refList OceanDNA-b38974/target_genomes_gtdb.txt --output OceanDNA-b38974/fastani_result_gtdb.tsv --threads 1
[2023-03-16 00:15:03,565] [INFO] Task succeeded: fastANI
[2023-03-16 00:15:03,576] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 00:15:03,576] [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_002934325.1	s__Marinobacter persicus_A	81.0109	542	894	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.99	99.99	0.99	0.99	3	-
GCF_900114155.1	s__Marinobacter persicus	80.9041	532	894	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.98	99.98	1.00	1.00	2	-
GCA_013393545.1	s__Marinobacter sp013393545	80.2374	452	894	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002258215.1	s__Marinobacter vinifirmus	79.8192	418	894	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	96.96	96.78	0.87	0.84	7	-
GCF_014201735.1	s__Marinobacter oulmenensis	79.3416	427	894	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000284615.1	s__Marinobacter hydrocarbonoclasticus	79.2177	402	894	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	97.10	96.48	0.88	0.81	26	-
GCA_003030785.1	s__Marinobacter sp003030785	78.9655	232	894	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002933275.1	s__Marinobacter maroccanus	78.9648	352	894	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114925.1	s__Marinobacter pelagius	78.9562	363	894	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018623515.1	s__Marinobacter sp018623515	78.8733	297	894	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003441595.1	s__Marinobacter sp003441595	78.8085	379	894	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115175.1	s__Marinobacter gudaonensis	78.8067	352	894	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002744735.1	s__Marinobacter guineae	78.7518	372	894	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001045555.1	s__Marinobacter subterrani	78.7064	376	894	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	97.05	97.05	0.84	0.84	2	-
GCF_000347775.1	s__Marinobacter santoriniensis	78.494	298	894	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000421165.1	s__Marinobacter daepoensis	78.4408	322	894	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.99	98.99	0.93	0.93	2	-
GCF_016427555.1	s__Marinobacter litoralis_A	78.213	301	894	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106945.1	s__Marinobacter mobilis	77.3951	203	894	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 00:15:03,578] [INFO] GTDB search result was written to OceanDNA-b38974/result_gtdb.tsv
[2023-03-16 00:15:03,579] [INFO] ===== GTDB Search completed =====
[2023-03-16 00:15:03,583] [INFO] DFAST_QC result json was written to OceanDNA-b38974/dqc_result.json
[2023-03-16 00:15:03,583] [INFO] DFAST_QC completed!
[2023-03-16 00:15:03,583] [INFO] Total running time: 0h1m31s