[2023-03-15 07:11:33,422] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:11:33,422] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:11:33,422] [INFO] DQC Reference Directory: /var/lib/cwl/stgf13a2574-37ff-4361-b92f-992c928cc64b/dqc_reference
[2023-03-15 07:11:34,535] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:11:34,536] [INFO] Task started: Prodigal
[2023-03-15 07:11:34,536] [INFO] Running command: cat /var/lib/cwl/stgd9a13abb-1353-4412-a926-df0360f1a8ad/OceanDNA-b35234.fa | prodigal -d OceanDNA-b35234/cds.fna -a OceanDNA-b35234/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:11:46,874] [INFO] Task succeeded: Prodigal
[2023-03-15 07:11:46,874] [INFO] Task started: HMMsearch
[2023-03-15 07:11:46,874] [INFO] Running command: hmmsearch --tblout OceanDNA-b35234/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf13a2574-37ff-4361-b92f-992c928cc64b/dqc_reference/reference_markers.hmm OceanDNA-b35234/protein.faa > /dev/null
[2023-03-15 07:11:47,110] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:11:47,111] [INFO] Found 6/6 markers.
[2023-03-15 07:11:47,136] [INFO] Query marker FASTA was written to OceanDNA-b35234/markers.fasta
[2023-03-15 07:11:47,137] [INFO] Task started: Blastn
[2023-03-15 07:11:47,137] [INFO] Running command: blastn -query OceanDNA-b35234/markers.fasta -db /var/lib/cwl/stgf13a2574-37ff-4361-b92f-992c928cc64b/dqc_reference/reference_markers.fasta -out OceanDNA-b35234/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:11:47,785] [INFO] Task succeeded: Blastn
[2023-03-15 07:11:47,786] [INFO] Selected 16 target genomes.
[2023-03-15 07:11:47,786] [INFO] Target genome list was writen to OceanDNA-b35234/target_genomes.txt
[2023-03-15 07:11:47,802] [INFO] Task started: fastANI
[2023-03-15 07:11:47,802] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9a13abb-1353-4412-a926-df0360f1a8ad/OceanDNA-b35234.fa --refList OceanDNA-b35234/target_genomes.txt --output OceanDNA-b35234/fastani_result.tsv --threads 1
[2023-03-15 07:12:00,652] [INFO] Task succeeded: fastANI
[2023-03-15 07:12:00,653] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf13a2574-37ff-4361-b92f-992c928cc64b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:12:00,653] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf13a2574-37ff-4361-b92f-992c928cc64b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:12:00,661] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2023-03-15 07:12:00,661] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 07:12:00,661] [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
Shewanella psychropiezotolerans	strain=YLB-06	GCA_007197555.1	2593655	2593655	type	True	99.1766	658	664	95	conclusive
Shewanella benthica	strain=DSM 8812	GCA_015069875.1	43661	43661	type	True	91.7297	454	664	95	below_threshold
Shewanella psychrophila	strain=WP2	GCA_002005305.1	225848	225848	type	True	87.7761	619	664	95	below_threshold
Shewanella violacea	strain=DSS12	GCA_000091325.1	60217	60217	type	True	86.5252	543	664	95	below_threshold
Shewanella eurypsychrophilus	strain=YLB-08	GCA_007004545.3	2593656	2593656	type	True	82.2764	467	664	95	below_threshold
Shewanella hanedai	strain=JCM 20706	GCA_007197645.1	25	25	type	True	79.5042	222	664	95	below_threshold
Shewanella abyssi	strain=DSM 17171	GCA_023284025.1	311789	311789	type	True	79.3555	146	664	95	below_threshold
Shewanella woodyi	strain=ATCC 51908	GCA_000019525.1	60961	60961	type	True	79.3492	241	664	95	below_threshold
Shewanella seohaensis	strain=KCTC 23556	GCA_025449215.1	755175	755175	type	True	78.5001	99	664	95	below_threshold
Shewanella seohaensis	strain=CCUG 60900	GCA_023283775.1	755175	755175	type	True	77.5604	99	664	95	below_threshold
Shewanella chilikensis	strain=KCTC 22540	GCA_014651975.1	558541	558541	type	True	77.424	85	664	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 07:12:00,662] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35234/tc_result.tsv
[2023-03-15 07:12:00,663] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:12:00,663] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:12:00,663] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf13a2574-37ff-4361-b92f-992c928cc64b/dqc_reference/checkm_data
[2023-03-15 07:12:00,664] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:12:00,754] [INFO] Task started: CheckM
[2023-03-15 07:12:00,754] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35234/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35234/checkm_input OceanDNA-b35234/checkm_result
[2023-03-15 07:12:36,408] [INFO] Task succeeded: CheckM
[2023-03-15 07:12:36,408] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 07:12:36,542] [INFO] ===== Completeness check finished =====
[2023-03-15 07:12:36,542] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:12:36,542] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35234/markers.fasta)
[2023-03-15 07:12:36,543] [INFO] Task started: Blastn
[2023-03-15 07:12:36,543] [INFO] Running command: blastn -query OceanDNA-b35234/markers.fasta -db /var/lib/cwl/stgf13a2574-37ff-4361-b92f-992c928cc64b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35234/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:12:37,415] [INFO] Task succeeded: Blastn
[2023-03-15 07:12:37,420] [INFO] Selected 7 target genomes.
[2023-03-15 07:12:37,420] [INFO] Target genome list was writen to OceanDNA-b35234/target_genomes_gtdb.txt
[2023-03-15 07:12:37,426] [INFO] Task started: fastANI
[2023-03-15 07:12:37,426] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9a13abb-1353-4412-a926-df0360f1a8ad/OceanDNA-b35234.fa --refList OceanDNA-b35234/target_genomes_gtdb.txt --output OceanDNA-b35234/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:12:44,154] [INFO] Task succeeded: fastANI
[2023-03-15 07:12:44,160] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 07:12:44,160] [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_007197555.1	s__Shewanella sp007197555	99.1766	658	664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.43	99.43	0.94	0.94	2	conclusive
GCF_015069875.1	s__Shewanella benthica	91.7326	454	664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	96.81	96.81	0.66	0.66	2	-
GCF_000172075.1	s__Shewanella benthica_A	90.2867	540	664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	96.25	96.25	0.86	0.86	2	-
GCA_013214165.1	s__Shewanella sp013214165	89.0046	521	664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002005305.1	s__Shewanella psychrophila	87.7761	619	664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000091325.1	s__Shewanella violacea	86.5252	543	664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007004545.2	s__Shewanella sp007004545	82.3924	450	664	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.97	99.97	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-03-15 07:12:44,162] [INFO] GTDB search result was written to OceanDNA-b35234/result_gtdb.tsv
[2023-03-15 07:12:44,164] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:12:44,168] [INFO] DFAST_QC result json was written to OceanDNA-b35234/dqc_result.json
[2023-03-15 07:12:44,169] [INFO] DFAST_QC completed!
[2023-03-15 07:12:44,169] [INFO] Total running time: 0h1m11s