[2023-03-18 04:39:31,339] [INFO] DFAST_QC pipeline started.
[2023-03-18 04:39:31,339] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 04:39:31,340] [INFO] DQC Reference Directory: /var/lib/cwl/stgec7940b8-a1d9-46cf-bd1d-ea726bcc0846/dqc_reference
[2023-03-18 04:39:32,484] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 04:39:32,484] [INFO] Task started: Prodigal
[2023-03-18 04:39:32,485] [INFO] Running command: cat /var/lib/cwl/stg8bf50f9d-27a2-4127-bb05-d619307b56e7/OceanDNA-b39062.fa | prodigal -d OceanDNA-b39062/cds.fna -a OceanDNA-b39062/protein.faa -g 11 -q > /dev/null
[2023-03-18 04:39:52,378] [INFO] Task succeeded: Prodigal
[2023-03-18 04:39:52,378] [INFO] Task started: HMMsearch
[2023-03-18 04:39:52,378] [INFO] Running command: hmmsearch --tblout OceanDNA-b39062/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgec7940b8-a1d9-46cf-bd1d-ea726bcc0846/dqc_reference/reference_markers.hmm OceanDNA-b39062/protein.faa > /dev/null
[2023-03-18 04:39:52,579] [INFO] Task succeeded: HMMsearch
[2023-03-18 04:39:52,580] [INFO] Found 6/6 markers.
[2023-03-18 04:39:52,599] [INFO] Query marker FASTA was written to OceanDNA-b39062/markers.fasta
[2023-03-18 04:39:52,600] [INFO] Task started: Blastn
[2023-03-18 04:39:52,600] [INFO] Running command: blastn -query OceanDNA-b39062/markers.fasta -db /var/lib/cwl/stgec7940b8-a1d9-46cf-bd1d-ea726bcc0846/dqc_reference/reference_markers.fasta -out OceanDNA-b39062/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:39:53,373] [INFO] Task succeeded: Blastn
[2023-03-18 04:39:53,374] [INFO] Selected 19 target genomes.
[2023-03-18 04:39:53,374] [INFO] Target genome list was writen to OceanDNA-b39062/target_genomes.txt
[2023-03-18 04:39:53,385] [INFO] Task started: fastANI
[2023-03-18 04:39:53,385] [INFO] Running command: fastANI --query /var/lib/cwl/stg8bf50f9d-27a2-4127-bb05-d619307b56e7/OceanDNA-b39062.fa --refList OceanDNA-b39062/target_genomes.txt --output OceanDNA-b39062/fastani_result.tsv --threads 1
[2023-03-18 04:40:07,981] [INFO] Task succeeded: fastANI
[2023-03-18 04:40:07,981] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgec7940b8-a1d9-46cf-bd1d-ea726bcc0846/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 04:40:07,981] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgec7940b8-a1d9-46cf-bd1d-ea726bcc0846/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 04:40:07,992] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 04:40:07,992] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 04:40:07,993] [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 lutaoensis	strain=T5054	GCA_001981305.1	135739	135739	type	True	99.0934	968	1057	95	conclusive
Marinobacter pelagius	strain=CGMCC 1.6775	GCA_900114925.1	379482	379482	type	True	80.5146	608	1057	95	below_threshold
Marinobacter gudaonensis	strain=CGMCC 1.6294	GCA_900115175.1	375760	375760	type	True	79.7329	542	1057	95	below_threshold
Marinobacter koreensis	strain=DSM 17924	GCA_023156285.1	335974	335974	type	True	79.7281	501	1057	95	below_threshold
Marinobacter santoriniensis	strain=NKSG1	GCA_000347775.1	523742	523742	type	True	79.7227	519	1057	95	below_threshold
Marinobacter vinifirmus	strain=FB1	GCA_002258215.1	355591	355591	type	True	79.5119	514	1057	95	below_threshold
Marinobacter oulmenensis	strain=DSM 22359	GCA_014201735.1	643747	643747	type	True	79.4049	460	1057	95	below_threshold
Marinobacter persicus	strain=IBRC-M 10445	GCA_900114155.1	930118	930118	type	True	79.3395	403	1057	95	below_threshold
Marinobacter persicus	strain=KCTC 23561	GCA_014652295.1	930118	930118	type	True	79.2388	419	1057	95	below_threshold
Marinobacter arenosus	strain=CAU 1620	GCA_019264345.1	2856822	2856822	type	True	79.1802	508	1057	95	below_threshold
Marinobacter profundi	strain=PWS21	GCA_002744715.1	2666256	2666256	type	True	79.1762	504	1057	95	below_threshold
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	79.0666	461	1057	95	below_threshold
Marinobacter subterrani	strain=JG233	GCA_001045555.1	1658765	1658765	type	True	79.04	549	1057	95	below_threshold
Marinobacter xestospongiae	strain=JCM 17469	GCA_023156385.1	994319	994319	type	True	78.9713	478	1057	95	below_threshold
Marinobacter guineae	strain=M3B	GCA_002744735.1	432303	432303	type	True	78.9584	501	1057	95	below_threshold
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	78.8343	466	1057	95	below_threshold
Marinobacter halodurans	strain=YJ-S3-2	GCA_004327985.1	2528979	2528979	type	True	78.7093	460	1057	95	below_threshold
Marinobacter mangrovi	strain=CHFG3-1-5	GCA_016798325.1	2803918	2803918	type	True	78.5695	462	1057	95	below_threshold
Marinobacter denitrificans	strain=JB02H27	GCA_008795955.1	2597703	2597703	type	True	78.3089	425	1057	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 04:40:07,993] [INFO] DFAST Taxonomy check result was written to OceanDNA-b39062/tc_result.tsv
[2023-03-18 04:40:07,993] [INFO] ===== Taxonomy check completed =====
[2023-03-18 04:40:07,993] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 04:40:07,993] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgec7940b8-a1d9-46cf-bd1d-ea726bcc0846/dqc_reference/checkm_data
[2023-03-18 04:40:07,994] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 04:40:07,998] [INFO] Task started: CheckM
[2023-03-18 04:40:07,998] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b39062/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b39062/checkm_input OceanDNA-b39062/checkm_result
[2023-03-18 04:40:58,535] [INFO] Task succeeded: CheckM
[2023-03-18 04:40:58,535] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.92%
Contamintation: 1.39%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 04:40:58,537] [INFO] ===== Completeness check finished =====
[2023-03-18 04:40:58,538] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:40:58,538] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b39062/markers.fasta)
[2023-03-18 04:40:58,539] [INFO] Task started: Blastn
[2023-03-18 04:40:58,539] [INFO] Running command: blastn -query OceanDNA-b39062/markers.fasta -db /var/lib/cwl/stgec7940b8-a1d9-46cf-bd1d-ea726bcc0846/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b39062/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:40:59,921] [INFO] Task succeeded: Blastn
[2023-03-18 04:40:59,922] [INFO] Selected 11 target genomes.
[2023-03-18 04:40:59,922] [INFO] Target genome list was writen to OceanDNA-b39062/target_genomes_gtdb.txt
[2023-03-18 04:40:59,968] [INFO] Task started: fastANI
[2023-03-18 04:40:59,968] [INFO] Running command: fastANI --query /var/lib/cwl/stg8bf50f9d-27a2-4127-bb05-d619307b56e7/OceanDNA-b39062.fa --refList OceanDNA-b39062/target_genomes_gtdb.txt --output OceanDNA-b39062/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:41:08,307] [INFO] Task succeeded: fastANI
[2023-03-18 04:41:08,314] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 04:41:08,315] [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_001981305.1	s__Marinobacter lutaoensis	99.0934	968	1057	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.21	99.12	0.92	0.92	6	conclusive
GCF_900114925.1	s__Marinobacter pelagius	80.5146	608	1057	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003315345.1	s__Marinobacter pelagius_A	80.3815	600	1057	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	80.2522	503	1057	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762755.1	s__Marinobacter sp014762755	80.0494	442	1057	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	79.7426	541	1057	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000347775.1	s__Marinobacter santoriniensis	79.7134	520	1057	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002934325.1	s__Marinobacter persicus_A	79.26	410	1057	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.99	99.99	0.99	0.99	3	-
GCF_002744715.1	s__Marinobacter profundi	79.1853	503	1057	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.28	99.28	0.94	0.94	2	-
GCF_004327985.1	s__Marinobacter_A halodurans	78.6844	462	1057	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003789045.1	s__Marinobacter_A sp003789045	78.5293	461	1057	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	97.70	97.70	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2023-03-18 04:41:08,315] [INFO] GTDB search result was written to OceanDNA-b39062/result_gtdb.tsv
[2023-03-18 04:41:08,315] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:41:08,317] [INFO] DFAST_QC result json was written to OceanDNA-b39062/dqc_result.json
[2023-03-18 04:41:08,317] [INFO] DFAST_QC completed!
[2023-03-18 04:41:08,317] [INFO] Total running time: 0h1m37s