[2023-03-18 07:54:29,618] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:54:29,619] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:54:29,619] [INFO] DQC Reference Directory: /var/lib/cwl/stga51d9c99-121d-4c90-919d-0bcee22e5667/dqc_reference
[2023-03-18 07:54:30,786] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:54:30,787] [INFO] Task started: Prodigal
[2023-03-18 07:54:30,787] [INFO] Running command: cat /var/lib/cwl/stgfc310f57-52d9-46eb-8f22-071c64d98bae/OceanDNA-b38979.fa | prodigal -d OceanDNA-b38979/cds.fna -a OceanDNA-b38979/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:54:54,012] [INFO] Task succeeded: Prodigal
[2023-03-18 07:54:54,013] [INFO] Task started: HMMsearch
[2023-03-18 07:54:54,013] [INFO] Running command: hmmsearch --tblout OceanDNA-b38979/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga51d9c99-121d-4c90-919d-0bcee22e5667/dqc_reference/reference_markers.hmm OceanDNA-b38979/protein.faa > /dev/null
[2023-03-18 07:54:54,235] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:54:54,236] [INFO] Found 6/6 markers.
[2023-03-18 07:54:54,263] [INFO] Query marker FASTA was written to OceanDNA-b38979/markers.fasta
[2023-03-18 07:54:54,264] [INFO] Task started: Blastn
[2023-03-18 07:54:54,264] [INFO] Running command: blastn -query OceanDNA-b38979/markers.fasta -db /var/lib/cwl/stga51d9c99-121d-4c90-919d-0bcee22e5667/dqc_reference/reference_markers.fasta -out OceanDNA-b38979/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:54:54,954] [INFO] Task succeeded: Blastn
[2023-03-18 07:54:54,956] [INFO] Selected 13 target genomes.
[2023-03-18 07:54:54,956] [INFO] Target genome list was writen to OceanDNA-b38979/target_genomes.txt
[2023-03-18 07:54:54,964] [INFO] Task started: fastANI
[2023-03-18 07:54:54,964] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc310f57-52d9-46eb-8f22-071c64d98bae/OceanDNA-b38979.fa --refList OceanDNA-b38979/target_genomes.txt --output OceanDNA-b38979/fastani_result.tsv --threads 1
[2023-03-18 07:55:05,964] [INFO] Task succeeded: fastANI
[2023-03-18 07:55:05,964] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga51d9c99-121d-4c90-919d-0bcee22e5667/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:55:05,964] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga51d9c99-121d-4c90-919d-0bcee22e5667/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:55:05,973] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:55:05,973] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 07:55:05,974] [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	87.9477	1066	1257	95	below_threshold
Marinobacter flavimaris	strain=KCTC 12185	GCA_003363485.1	262076	262076	type	True	86.8029	1044	1257	95	below_threshold
Marinobacter flavimaris	strain=LMG 23834	GCA_002933295.1	262076	262076	type	True	86.7378	1059	1257	95	below_threshold
Marinobacter adhaerens	strain=HP15	GCA_000166295.1	1033846	1033846	type	True	86.5585	1046	1257	95	below_threshold
Marinobacter guineae	strain=M3B	GCA_002744735.1	432303	432303	type	True	82.3053	860	1257	95	below_threshold
Marinobacter subterrani	strain=JG233	GCA_001045555.1	1658765	1658765	type	True	82.273	852	1257	95	below_threshold
Marinobacter gudaonensis	strain=CGMCC 1.6294	GCA_900115175.1	375760	375760	type	True	81.8161	790	1257	95	below_threshold
Marinobacter pelagius	strain=CGMCC 1.6775	GCA_900114925.1	379482	379482	type	True	80.6086	637	1257	95	below_threshold
Marinobacter arenosus	strain=CAU 1620	GCA_019264345.1	2856822	2856822	type	True	80.2833	665	1257	95	below_threshold
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	79.9083	612	1257	95	below_threshold
Marinobacter bryozoorum	strain=DSM 15401	GCA_023156245.1	256324	256324	type	True	79.0252	330	1257	95	below_threshold
Alcanivorax marinus	strain=R8-12	GCA_025532125.1	1177169	1177169	type	True	76.5367	98	1257	95	below_threshold
Marinobacterium arenosum	strain=CAU 1594	GCA_019795155.1	2862496	2862496	type	True	76.1758	79	1257	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 07:55:05,974] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38979/tc_result.tsv
[2023-03-18 07:55:05,974] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:55:05,974] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:55:05,974] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga51d9c99-121d-4c90-919d-0bcee22e5667/dqc_reference/checkm_data
[2023-03-18 07:55:05,975] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:55:05,980] [INFO] Task started: CheckM
[2023-03-18 07:55:05,981] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38979/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38979/checkm_input OceanDNA-b38979/checkm_result
[2023-03-18 07:56:03,960] [INFO] Task succeeded: CheckM
[2023-03-18 07:56:03,960] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 07:56:03,963] [INFO] ===== Completeness check finished =====
[2023-03-18 07:56:03,963] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:56:03,963] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38979/markers.fasta)
[2023-03-18 07:56:03,971] [INFO] Task started: Blastn
[2023-03-18 07:56:03,971] [INFO] Running command: blastn -query OceanDNA-b38979/markers.fasta -db /var/lib/cwl/stga51d9c99-121d-4c90-919d-0bcee22e5667/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38979/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:56:05,002] [INFO] Task succeeded: Blastn
[2023-03-18 07:56:05,003] [INFO] Selected 10 target genomes.
[2023-03-18 07:56:05,003] [INFO] Target genome list was writen to OceanDNA-b38979/target_genomes_gtdb.txt
[2023-03-18 07:56:05,014] [INFO] Task started: fastANI
[2023-03-18 07:56:05,014] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc310f57-52d9-46eb-8f22-071c64d98bae/OceanDNA-b38979.fa --refList OceanDNA-b38979/target_genomes_gtdb.txt --output OceanDNA-b38979/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:56:14,159] [INFO] Task succeeded: fastANI
[2023-03-18 07:56:14,166] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 07:56:14,166] [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_009617755.1	s__Marinobacter salsuginis	97.4084	1121	1257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	97.38	96.64	0.89	0.80	12	conclusive
GCF_001650915.1	s__Marinobacter sp001650915	88.3107	1072	1257	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	87.9566	1065	1257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003030785.1	s__Marinobacter sp003030785	87.1473	612	1257	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	86.8675	1032	1257	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	86.7378	1059	1257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	96.6719	97.80	96.90	0.89	0.83	14	-
GCF_900188435.1	s__Marinobacter sp900188435	86.684	994	1257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008107725.1	s__Marinobacter sp008107725	86.6619	1038	1257	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	86.5675	1045	1257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	96.6719	98.39	97.71	0.91	0.87	5	-
GCF_900188315.1	s__Marinobacter sp900188315	86.1842	983	1257	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.8497	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 07:56:14,167] [INFO] GTDB search result was written to OceanDNA-b38979/result_gtdb.tsv
[2023-03-18 07:56:14,167] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:56:14,168] [INFO] DFAST_QC result json was written to OceanDNA-b38979/dqc_result.json
[2023-03-18 07:56:14,168] [INFO] DFAST_QC completed!
[2023-03-18 07:56:14,168] [INFO] Total running time: 0h1m45s