[2023-03-18 23:03:14,054] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:03:14,054] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:03:14,054] [INFO] DQC Reference Directory: /var/lib/cwl/stg36a4276c-cae5-4a18-878c-b76ce23347a2/dqc_reference
[2023-03-18 23:03:15,189] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:03:15,189] [INFO] Task started: Prodigal
[2023-03-18 23:03:15,189] [INFO] Running command: cat /var/lib/cwl/stg69f1e9f8-ff1a-49b0-af65-a6401f1ca6ed/OceanDNA-b38966.fa | prodigal -d OceanDNA-b38966/cds.fna -a OceanDNA-b38966/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:03:30,970] [INFO] Task succeeded: Prodigal
[2023-03-18 23:03:30,971] [INFO] Task started: HMMsearch
[2023-03-18 23:03:30,971] [INFO] Running command: hmmsearch --tblout OceanDNA-b38966/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg36a4276c-cae5-4a18-878c-b76ce23347a2/dqc_reference/reference_markers.hmm OceanDNA-b38966/protein.faa > /dev/null
[2023-03-18 23:03:31,190] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:03:31,191] [INFO] Found 6/6 markers.
[2023-03-18 23:03:31,218] [INFO] Query marker FASTA was written to OceanDNA-b38966/markers.fasta
[2023-03-18 23:03:31,219] [INFO] Task started: Blastn
[2023-03-18 23:03:31,219] [INFO] Running command: blastn -query OceanDNA-b38966/markers.fasta -db /var/lib/cwl/stg36a4276c-cae5-4a18-878c-b76ce23347a2/dqc_reference/reference_markers.fasta -out OceanDNA-b38966/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:03:31,878] [INFO] Task succeeded: Blastn
[2023-03-18 23:03:31,881] [INFO] Selected 16 target genomes.
[2023-03-18 23:03:31,881] [INFO] Target genome list was writen to OceanDNA-b38966/target_genomes.txt
[2023-03-18 23:03:31,889] [INFO] Task started: fastANI
[2023-03-18 23:03:31,889] [INFO] Running command: fastANI --query /var/lib/cwl/stg69f1e9f8-ff1a-49b0-af65-a6401f1ca6ed/OceanDNA-b38966.fa --refList OceanDNA-b38966/target_genomes.txt --output OceanDNA-b38966/fastani_result.tsv --threads 1
[2023-03-18 23:03:43,564] [INFO] Task succeeded: fastANI
[2023-03-18 23:03:43,564] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg36a4276c-cae5-4a18-878c-b76ce23347a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:03:43,564] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg36a4276c-cae5-4a18-878c-b76ce23347a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:03:43,574] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:03:43,574] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 23:03:43,574] [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 maroccanus	strain=N4	GCA_002933275.1	2055143	2055143	type	True	90.6146	681	776	95	below_threshold
Marinobacter flavimaris	strain=KCTC 12185	GCA_003363485.1	262076	262076	type	True	88.9422	683	776	95	below_threshold
Marinobacter flavimaris	strain=LMG 23834	GCA_002933295.1	262076	262076	type	True	88.9177	683	776	95	below_threshold
Marinobacter adhaerens	strain=HP15	GCA_000166295.1	1033846	1033846	type	True	87.3079	665	776	95	below_threshold
Marinobacter subterrani	strain=JG233	GCA_001045555.1	1658765	1658765	type	True	82.8132	562	776	95	below_threshold
Marinobacter guineae	strain=M3B	GCA_002744735.1	432303	432303	type	True	82.6332	593	776	95	below_threshold
Marinobacter gudaonensis	strain=CGMCC 1.6294	GCA_900115175.1	375760	375760	type	True	81.4187	518	776	95	below_threshold
Marinobacter pelagius	strain=CGMCC 1.6775	GCA_900114925.1	379482	379482	type	True	80.5645	426	776	95	below_threshold
Marinobacter arenosus	strain=CAU 1620	GCA_019264345.1	2856822	2856822	type	True	80.0168	420	776	95	below_threshold
Marinobacter sediminum	strain=R65	GCA_016820575.1	256323	256323	type	True	79.6841	390	776	95	below_threshold
Marinobacter shengliensis	strain=SL013A34A2	GCA_003007715.1	1389223	1389223	type	True	79.6114	359	776	95	below_threshold
Marinobacter denitrificans	strain=JB02H27	GCA_008795955.1	2597703	2597703	type	True	79.231	356	776	95	below_threshold
Marinobacter salinexigens	strain=ZYF650	GCA_008370345.1	2919747	2919747	type	True	79.1772	318	776	95	below_threshold
Marinobacter algicola	strain=DG893	GCA_000170835.1	236100	236100	type	True	79.0901	338	776	95	below_threshold
Marinobacter xestospongiae	strain=JCM 17469	GCA_023156385.1	994319	994319	type	True	78.1435	252	776	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 23:03:43,576] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38966/tc_result.tsv
[2023-03-18 23:03:43,577] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:03:43,577] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:03:43,577] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg36a4276c-cae5-4a18-878c-b76ce23347a2/dqc_reference/checkm_data
[2023-03-18 23:03:43,578] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:03:43,584] [INFO] Task started: CheckM
[2023-03-18 23:03:43,584] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38966/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38966/checkm_input OceanDNA-b38966/checkm_result
[2023-03-18 23:04:25,493] [INFO] Task succeeded: CheckM
[2023-03-18 23:04:25,493] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.49%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:04:25,496] [INFO] ===== Completeness check finished =====
[2023-03-18 23:04:25,496] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:04:25,496] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38966/markers.fasta)
[2023-03-18 23:04:25,497] [INFO] Task started: Blastn
[2023-03-18 23:04:25,497] [INFO] Running command: blastn -query OceanDNA-b38966/markers.fasta -db /var/lib/cwl/stg36a4276c-cae5-4a18-878c-b76ce23347a2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38966/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:04:26,578] [INFO] Task succeeded: Blastn
[2023-03-18 23:04:26,579] [INFO] Selected 9 target genomes.
[2023-03-18 23:04:26,579] [INFO] Target genome list was writen to OceanDNA-b38966/target_genomes_gtdb.txt
[2023-03-18 23:04:26,588] [INFO] Task started: fastANI
[2023-03-18 23:04:26,588] [INFO] Running command: fastANI --query /var/lib/cwl/stg69f1e9f8-ff1a-49b0-af65-a6401f1ca6ed/OceanDNA-b38966.fa --refList OceanDNA-b38966/target_genomes_gtdb.txt --output OceanDNA-b38966/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:04:33,745] [INFO] Task succeeded: fastANI
[2023-03-18 23:04:33,751] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 23:04:33,751] [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_003030785.1	s__Marinobacter sp003030785	96.6572	428	776	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001650915.1	s__Marinobacter sp001650915	91.2418	686	776	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.33	97.47	0.91	0.86	4	-
GCF_002933275.1	s__Marinobacter maroccanus	90.6146	681	776	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000235625.1	s__Marinobacter manganoxydans_A	90.0435	688	776	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	96.5877	97.20	96.90	0.83	0.80	5	-
GCF_002933295.1	s__Marinobacter flavimaris	88.9177	683	776	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	96.6719	97.80	96.90	0.89	0.83	14	-
GCF_008107725.1	s__Marinobacter sp008107725	88.3127	661	776	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188435.1	s__Marinobacter sp900188435	88.0206	650	776	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000166295.1	s__Marinobacter adhaerens	87.3079	665	776	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	96.6719	98.39	97.71	0.91	0.87	5	-
GCF_009617755.1	s__Marinobacter salsuginis	87.1525	645	776	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	97.38	96.64	0.89	0.80	12	-
--------------------------------------------------------------------------------
[2023-03-18 23:04:33,752] [INFO] GTDB search result was written to OceanDNA-b38966/result_gtdb.tsv
[2023-03-18 23:04:33,752] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:04:33,753] [INFO] DFAST_QC result json was written to OceanDNA-b38966/dqc_result.json
[2023-03-18 23:04:33,753] [INFO] DFAST_QC completed!
[2023-03-18 23:04:33,753] [INFO] Total running time: 0h1m20s