[2023-03-15 11:22:20,468] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:22:20,468] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:22:20,468] [INFO] DQC Reference Directory: /var/lib/cwl/stg41a56a18-e5a2-4417-9dcc-25d7b628220e/dqc_reference
[2023-03-15 11:22:21,954] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:22:21,956] [INFO] Task started: Prodigal
[2023-03-15 11:22:21,956] [INFO] Running command: cat /var/lib/cwl/stgec3587bc-a507-4a3f-a38e-6c8023e95826/OceanDNA-b41011.fa | prodigal -d OceanDNA-b41011/cds.fna -a OceanDNA-b41011/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:22:50,854] [INFO] Task succeeded: Prodigal
[2023-03-15 11:22:50,855] [INFO] Task started: HMMsearch
[2023-03-15 11:22:50,855] [INFO] Running command: hmmsearch --tblout OceanDNA-b41011/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg41a56a18-e5a2-4417-9dcc-25d7b628220e/dqc_reference/reference_markers.hmm OceanDNA-b41011/protein.faa > /dev/null
[2023-03-15 11:22:51,101] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:22:51,101] [INFO] Found 6/6 markers.
[2023-03-15 11:22:51,134] [INFO] Query marker FASTA was written to OceanDNA-b41011/markers.fasta
[2023-03-15 11:22:51,135] [INFO] Task started: Blastn
[2023-03-15 11:22:51,135] [INFO] Running command: blastn -query OceanDNA-b41011/markers.fasta -db /var/lib/cwl/stg41a56a18-e5a2-4417-9dcc-25d7b628220e/dqc_reference/reference_markers.fasta -out OceanDNA-b41011/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:22:51,901] [INFO] Task succeeded: Blastn
[2023-03-15 11:22:51,902] [INFO] Selected 15 target genomes.
[2023-03-15 11:22:51,902] [INFO] Target genome list was writen to OceanDNA-b41011/target_genomes.txt
[2023-03-15 11:22:51,913] [INFO] Task started: fastANI
[2023-03-15 11:22:51,913] [INFO] Running command: fastANI --query /var/lib/cwl/stgec3587bc-a507-4a3f-a38e-6c8023e95826/OceanDNA-b41011.fa --refList OceanDNA-b41011/target_genomes.txt --output OceanDNA-b41011/fastani_result.tsv --threads 1
[2023-03-15 11:23:04,422] [INFO] Task succeeded: fastANI
[2023-03-15 11:23:04,422] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg41a56a18-e5a2-4417-9dcc-25d7b628220e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:23:04,423] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg41a56a18-e5a2-4417-9dcc-25d7b628220e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:23:04,433] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2023-03-15 11:23:04,433] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 11:23:04,433] [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
Pseudomonas zeshuii	strain=KACC 15471	GCA_900141925.1	1076620	1076620	type	True	97.4613	1375	1599	95	conclusive
Pseudomonas asuensis	strain=JCM 13501	GCA_014646755.1	1825787	1825787	type	True	85.1586	1175	1599	95	below_threshold
Pseudomonas duriflava	strain=CGMCC 1.6858	GCA_007830155.1	459528	459528	type	True	79.6751	566	1599	95	below_threshold
Pseudomonas psychrotolerans	strain=DSM 15758	GCA_900102665.1	237610	237610	suspected-type	True	77.6497	321	1599	95	below_threshold
Pseudomonas oryzihabitans	strain=DSM 6835	GCA_012986195.1	47885	47885	suspected-type	True	77.6401	324	1599	95	below_threshold
Pseudomonas psychrotolerans	strain=DSM 15758	GCA_012985915.1	237610	237610	suspected-type	True	77.622	325	1599	95	below_threshold
Pseudomonas oryzihabitans	strain=NBRC 102199	GCA_000730625.1	47885	47885	suspected-type	True	77.576	323	1599	95	below_threshold
Pseudomonas rhizoryzae	strain=RY24	GCA_005250615.1	2571129	2571129	type	True	77.3175	320	1599	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_021602465.1	2740517	2740517	suspected-type	True	77.2919	252	1599	95	below_threshold
Pseudomonas alcaligenes	strain=NCTC10367	GCA_900455475.1	43263	43263	type	True	77.0529	200	1599	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	76.9897	247	1599	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	76.9599	256	1599	95	below_threshold
Serpens gallinarum	strain=Sa2CUA2	GCA_014836765.1	2763075	2763075	type	True	76.8929	161	1599	95	below_threshold
Pseudomonas pohangensis	strain=DSM 17875	GCA_900105995.1	364197	364197	type	True	76.8929	145	1599	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	76.8925	263	1599	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 11:23:04,433] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41011/tc_result.tsv
[2023-03-15 11:23:04,433] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:23:04,434] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:23:04,434] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg41a56a18-e5a2-4417-9dcc-25d7b628220e/dqc_reference/checkm_data
[2023-03-15 11:23:04,434] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:23:04,447] [INFO] Task started: CheckM
[2023-03-15 11:23:04,447] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41011/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41011/checkm_input OceanDNA-b41011/checkm_result
[2023-03-15 11:24:15,566] [INFO] Task succeeded: CheckM
[2023-03-15 11:24:15,566] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.69%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:24:15,569] [INFO] ===== Completeness check finished =====
[2023-03-15 11:24:15,569] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:24:15,570] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41011/markers.fasta)
[2023-03-15 11:24:15,571] [INFO] Task started: Blastn
[2023-03-15 11:24:15,571] [INFO] Running command: blastn -query OceanDNA-b41011/markers.fasta -db /var/lib/cwl/stg41a56a18-e5a2-4417-9dcc-25d7b628220e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41011/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:24:16,837] [INFO] Task succeeded: Blastn
[2023-03-15 11:24:16,838] [INFO] Selected 15 target genomes.
[2023-03-15 11:24:16,838] [INFO] Target genome list was writen to OceanDNA-b41011/target_genomes_gtdb.txt
[2023-03-15 11:24:16,849] [INFO] Task started: fastANI
[2023-03-15 11:24:16,849] [INFO] Running command: fastANI --query /var/lib/cwl/stgec3587bc-a507-4a3f-a38e-6c8023e95826/OceanDNA-b41011.fa --refList OceanDNA-b41011/target_genomes_gtdb.txt --output OceanDNA-b41011/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:24:30,495] [INFO] Task succeeded: fastANI
[2023-03-15 11:24:30,504] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 11:24:30,505] [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_002091675.1	s__Pseudomonas_B luteola	97.3921	1336	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	98.05	97.34	0.90	0.85	19	conclusive
GCF_014646755.1	s__Pseudomonas_B asuensis	85.1586	1175	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830155.1	s__Pseudomonas_B duriflava	79.6751	566	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000730625.1	s__Pseudomonas_B oryzihabitans	77.5792	324	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	97.97	96.38	0.92	0.87	28	-
GCF_001518815.1	s__Pseudomonas_B oryzihabitans_E	77.5476	297	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	98.13	98.08	0.95	0.93	4	-
GCF_007665395.1	s__Pseudomonas_B psychrotolerans_C	77.529	308	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006384975.1	s__Pseudomonas_B psychrotolerans_B	77.4977	302	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650425.1	s__Pseudomonas_B oryzihabitans_B	77.4367	312	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	97.78	97.39	0.90	0.88	6	-
GCF_001512295.1	s__Pseudomonas_B sp001512295	77.4184	302	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005250615.1	s__Pseudomonas_B rhizoryzae	77.325	320	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	98.30	97.74	0.93	0.89	15	-
GCF_008807375.1	s__Pseudomonas_F lalkuanensis	77.2618	223	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017491605.1	s__Pseudomonas sp017491605	77.1504	241	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009189165.1	s__Pseudomonas sp009189165	77.0356	237	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014836765.1	s__Pseudomonas_H sp014836765	76.8929	161	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_H	95.0	97.71	97.71	0.94	0.94	2	-
GCF_000213805.1	s__Pseudomonas_E fulva_B	76.7113	233	1599	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.53	96.12	0.92	0.90	6	-
--------------------------------------------------------------------------------
[2023-03-15 11:24:30,505] [INFO] GTDB search result was written to OceanDNA-b41011/result_gtdb.tsv
[2023-03-15 11:24:30,505] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:24:30,507] [INFO] DFAST_QC result json was written to OceanDNA-b41011/dqc_result.json
[2023-03-15 11:24:30,507] [INFO] DFAST_QC completed!
[2023-03-15 11:24:30,507] [INFO] Total running time: 0h2m10s