[2023-03-14 12:24:50,634] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:24:50,634] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:24:50,634] [INFO] DQC Reference Directory: /var/lib/cwl/stg60478dae-fd51-460b-8a90-44120213e114/dqc_reference
[2023-03-14 12:24:51,774] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:24:51,775] [INFO] Task started: Prodigal
[2023-03-14 12:24:51,775] [INFO] Running command: cat /var/lib/cwl/stg4048dcb5-b80f-41dc-8e9d-316a07880c0a/OceanDNA-b9764.fa | prodigal -d OceanDNA-b9764/cds.fna -a OceanDNA-b9764/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:25:16,163] [INFO] Task succeeded: Prodigal
[2023-03-14 12:25:16,163] [INFO] Task started: HMMsearch
[2023-03-14 12:25:16,163] [INFO] Running command: hmmsearch --tblout OceanDNA-b9764/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg60478dae-fd51-460b-8a90-44120213e114/dqc_reference/reference_markers.hmm OceanDNA-b9764/protein.faa > /dev/null
[2023-03-14 12:25:16,380] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:25:16,380] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4048dcb5-b80f-41dc-8e9d-316a07880c0a/OceanDNA-b9764.fa]
[2023-03-14 12:25:16,407] [INFO] Query marker FASTA was written to OceanDNA-b9764/markers.fasta
[2023-03-14 12:25:16,409] [INFO] Task started: Blastn
[2023-03-14 12:25:16,409] [INFO] Running command: blastn -query OceanDNA-b9764/markers.fasta -db /var/lib/cwl/stg60478dae-fd51-460b-8a90-44120213e114/dqc_reference/reference_markers.fasta -out OceanDNA-b9764/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:25:16,995] [INFO] Task succeeded: Blastn
[2023-03-14 12:25:16,995] [INFO] Selected 13 target genomes.
[2023-03-14 12:25:16,996] [INFO] Target genome list was writen to OceanDNA-b9764/target_genomes.txt
[2023-03-14 12:25:17,002] [INFO] Task started: fastANI
[2023-03-14 12:25:17,002] [INFO] Running command: fastANI --query /var/lib/cwl/stg4048dcb5-b80f-41dc-8e9d-316a07880c0a/OceanDNA-b9764.fa --refList OceanDNA-b9764/target_genomes.txt --output OceanDNA-b9764/fastani_result.tsv --threads 1
[2023-03-14 12:25:25,792] [INFO] Task succeeded: fastANI
[2023-03-14 12:25:25,792] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg60478dae-fd51-460b-8a90-44120213e114/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:25:25,792] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg60478dae-fd51-460b-8a90-44120213e114/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:25:25,806] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:25:25,807] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 12:25:25,807] [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
Muricauda sediminis	strain=40Bstr401	GCA_010500845.1	2696468	2696468	type	True	87.5289	750	899	95	below_threshold
Muricauda maritima	strain=72	GCA_008017365.1	2306998	2306998	type	True	86.6615	730	899	95	below_threshold
Muricauda maritima	strain=72	GCA_003584135.1	2306998	2306998	type	True	86.6615	730	899	95	below_threshold
Muricauda aequoris	strain=NH166	GCA_008017345.1	2306997	2306997	type	True	86.5748	736	899	95	below_threshold
Muricauda aequoris	strain=NH166	GCA_003584165.1	2306997	2306997	type	True	86.5748	736	899	95	below_threshold
Muricauda hadalis	strain=MT-229	GCA_007785775.2	2597517	2597517	type	True	79.668	458	899	95	below_threshold
Muricauda beolgyonensis	strain=KCTC 23501	GCA_003992615.1	864064	864064	type	True	79.6501	500	899	95	below_threshold
Muricauda profundi	strain=BC31-3-A3	GCA_017313275.1	2915620	2915620	type	True	78.3902	383	899	95	below_threshold
Muricauda aurea	strain=BC31-1-A7	GCA_017313785.1	2915619	2915619	type	True	78.3327	379	899	95	below_threshold
Muricauda flava	strain=DSM 22638	GCA_900129665.1	570519	570519	type	True	76.9504	176	899	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 12:25:25,807] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9764/tc_result.tsv
[2023-03-14 12:25:25,807] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:25:25,807] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:25:25,807] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg60478dae-fd51-460b-8a90-44120213e114/dqc_reference/checkm_data
[2023-03-14 12:25:25,808] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:25:25,816] [INFO] Task started: CheckM
[2023-03-14 12:25:25,816] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9764/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9764/checkm_input OceanDNA-b9764/checkm_result
[2023-03-14 12:26:28,411] [INFO] Task succeeded: CheckM
[2023-03-14 12:26:28,412] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 12:26:28,452] [INFO] ===== Completeness check finished =====
[2023-03-14 12:26:28,452] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:26:28,452] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9764/markers.fasta)
[2023-03-14 12:26:28,454] [INFO] Task started: Blastn
[2023-03-14 12:26:28,454] [INFO] Running command: blastn -query OceanDNA-b9764/markers.fasta -db /var/lib/cwl/stg60478dae-fd51-460b-8a90-44120213e114/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9764/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:26:29,347] [INFO] Task succeeded: Blastn
[2023-03-14 12:26:29,366] [INFO] Selected 12 target genomes.
[2023-03-14 12:26:29,366] [INFO] Target genome list was writen to OceanDNA-b9764/target_genomes_gtdb.txt
[2023-03-14 12:26:29,380] [INFO] Task started: fastANI
[2023-03-14 12:26:29,380] [INFO] Running command: fastANI --query /var/lib/cwl/stg4048dcb5-b80f-41dc-8e9d-316a07880c0a/OceanDNA-b9764.fa --refList OceanDNA-b9764/target_genomes_gtdb.txt --output OceanDNA-b9764/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:26:38,060] [INFO] Task succeeded: fastANI
[2023-03-14 12:26:38,067] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 12:26:38,067] [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_010500845.1	s__Muricauda sediminis	87.5289	750	899	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003584135.1	s__Muricauda sp003584135	86.6615	730	899	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003584165.1	s__Muricauda sp003584165	86.5748	736	899	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003058265.1	s__Muricauda sp003058265	80.1564	482	899	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007785775.2	s__Muricauda sp003973595	79.668	458	899	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	98.36	98.36	0.87	0.87	2	-
GCF_003992615.1	s__Muricauda beolgyonensis	79.6606	499	899	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102925.1	s__Muricauda zhangzhouensis	79.0072	391	899	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001683915.1	s__Muricauda sp001683915	78.9362	375	899	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	99.66	99.66	0.95	0.95	2	-
GCF_000745185.1	s__Muricauda sp000745185	78.6397	364	899	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017313275.1	s__Muricauda lutimaris_A	78.3802	384	899	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017313785.1	s__Muricauda sp002711825	78.3428	378	899	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	98.76	98.31	0.81	0.77	4	-
GCF_017313105.1	s__Muricauda sp017313105	78.2388	364	899	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 12:26:38,067] [INFO] GTDB search result was written to OceanDNA-b9764/result_gtdb.tsv
[2023-03-14 12:26:38,068] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:26:38,069] [INFO] DFAST_QC result json was written to OceanDNA-b9764/dqc_result.json
[2023-03-14 12:26:38,069] [INFO] DFAST_QC completed!
[2023-03-14 12:26:38,069] [INFO] Total running time: 0h1m47s