[2023-03-16 09:26:56,794] [INFO] DFAST_QC pipeline started.
[2023-03-16 09:26:56,796] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 09:26:56,796] [INFO] DQC Reference Directory: /var/lib/cwl/stgd38249d8-a72b-4969-88b5-c09ce5b655f8/dqc_reference
[2023-03-16 09:26:57,901] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 09:26:57,902] [INFO] Task started: Prodigal
[2023-03-16 09:26:57,902] [INFO] Running command: cat /var/lib/cwl/stg9d2349e6-b8b3-41c4-b9f4-bf41d6ac73e2/OceanDNA-b30153.fa | prodigal -d OceanDNA-b30153/cds.fna -a OceanDNA-b30153/protein.faa -g 11 -q > /dev/null
[2023-03-16 09:27:31,059] [INFO] Task succeeded: Prodigal
[2023-03-16 09:27:31,059] [INFO] Task started: HMMsearch
[2023-03-16 09:27:31,060] [INFO] Running command: hmmsearch --tblout OceanDNA-b30153/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd38249d8-a72b-4969-88b5-c09ce5b655f8/dqc_reference/reference_markers.hmm OceanDNA-b30153/protein.faa > /dev/null
[2023-03-16 09:27:31,307] [INFO] Task succeeded: HMMsearch
[2023-03-16 09:27:31,308] [INFO] Found 6/6 markers.
[2023-03-16 09:27:31,373] [INFO] Query marker FASTA was written to OceanDNA-b30153/markers.fasta
[2023-03-16 09:27:31,374] [INFO] Task started: Blastn
[2023-03-16 09:27:31,374] [INFO] Running command: blastn -query OceanDNA-b30153/markers.fasta -db /var/lib/cwl/stgd38249d8-a72b-4969-88b5-c09ce5b655f8/dqc_reference/reference_markers.fasta -out OceanDNA-b30153/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:27:32,285] [INFO] Task succeeded: Blastn
[2023-03-16 09:27:32,286] [INFO] Selected 13 target genomes.
[2023-03-16 09:27:32,286] [INFO] Target genome list was writen to OceanDNA-b30153/target_genomes.txt
[2023-03-16 09:27:32,294] [INFO] Task started: fastANI
[2023-03-16 09:27:32,294] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d2349e6-b8b3-41c4-b9f4-bf41d6ac73e2/OceanDNA-b30153.fa --refList OceanDNA-b30153/target_genomes.txt --output OceanDNA-b30153/fastani_result.tsv --threads 1
[2023-03-16 09:27:46,632] [INFO] Task succeeded: fastANI
[2023-03-16 09:27:46,632] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd38249d8-a72b-4969-88b5-c09ce5b655f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 09:27:46,633] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd38249d8-a72b-4969-88b5-c09ce5b655f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 09:27:46,641] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2023-03-16 09:27:46,641] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-16 09:27:46,641] [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
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	95.8065	1558	1795	95	conclusive
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	85.1444	1119	1795	95	below_threshold
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	85.0369	1080	1795	95	below_threshold
Salipiger profundus	strain=JLT2016	GCA_001969385.1	1229727	1229727	type	True	84.9801	1131	1795	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	82.5491	1022	1795	95	below_threshold
Yangia pacifica	strain=CGMCC 1.3455	GCA_900100725.1	311180	311180	suspected-type	True	82.4961	1024	1795	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	82.1683	905	1795	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	80.8371	897	1795	95	below_threshold
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	80.104	712	1795	95	below_threshold
Salipiger aestuarii	strain=AD8	GCA_008930655.1	568098	568098	type	True	80.0802	788	1795	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	78.9092	535	1795	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	78.7922	549	1795	95	below_threshold
Mameliella sediminis	strain=DP3N28-2	GCA_019218285.1	2836866	2836866	type	True	78.5018	560	1795	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 09:27:46,652] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30153/tc_result.tsv
[2023-03-16 09:27:46,669] [INFO] ===== Taxonomy check completed =====
[2023-03-16 09:27:46,669] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 09:27:46,669] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd38249d8-a72b-4969-88b5-c09ce5b655f8/dqc_reference/checkm_data
[2023-03-16 09:27:46,670] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 09:27:46,676] [INFO] Task started: CheckM
[2023-03-16 09:27:46,677] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30153/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30153/checkm_input OceanDNA-b30153/checkm_result
[2023-03-16 09:29:15,216] [INFO] Task succeeded: CheckM
[2023-03-16 09:29:15,216] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 09:29:15,237] [INFO] ===== Completeness check finished =====
[2023-03-16 09:29:15,237] [INFO] ===== Start GTDB Search =====
[2023-03-16 09:29:15,237] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30153/markers.fasta)
[2023-03-16 09:29:15,238] [INFO] Task started: Blastn
[2023-03-16 09:29:15,238] [INFO] Running command: blastn -query OceanDNA-b30153/markers.fasta -db /var/lib/cwl/stgd38249d8-a72b-4969-88b5-c09ce5b655f8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30153/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:29:16,870] [INFO] Task succeeded: Blastn
[2023-03-16 09:29:16,878] [INFO] Selected 10 target genomes.
[2023-03-16 09:29:16,879] [INFO] Target genome list was writen to OceanDNA-b30153/target_genomes_gtdb.txt
[2023-03-16 09:29:16,884] [INFO] Task started: fastANI
[2023-03-16 09:29:16,884] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d2349e6-b8b3-41c4-b9f4-bf41d6ac73e2/OceanDNA-b30153.fa --refList OceanDNA-b30153/target_genomes_gtdb.txt --output OceanDNA-b30153/fastani_result_gtdb.tsv --threads 1
[2023-03-16 09:29:29,009] [INFO] Task succeeded: fastANI
[2023-03-16 09:29:29,016] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 09:29:29,016] [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_900102075.1	s__Salipiger thiooxidans	95.8065	1558	1795	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.34	95.88	0.90	0.85	6	conclusive
GCF_000153725.1	s__Salipiger bermudensis	85.1444	1119	1795	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.06	97.75	0.87	0.75	4	-
GCF_001969385.1	s__Salipiger profundus	84.9952	1130	1795	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	99.85	99.64	0.97	0.94	5	-
GCF_017311415.1	s__Salipiger abyssi_A	83.8186	997	1795	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975705.1	s__Salipiger abyssi	83.8074	1023	1795	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002300555.1	s__Salipiger sp002300555	82.9144	738	1795	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000442255.1	s__Salipiger mucosus	82.6104	935	1795	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003111685.1	s__Salipiger pacificus_A	82.5073	966	1795	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.69	97.64	0.90	0.89	3	-
GCF_014643635.1	s__Salipiger pallidus	82.1599	906	1795	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860705.1	s__Salipiger sp018860705	80.9791	909	1795	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 09:29:29,016] [INFO] GTDB search result was written to OceanDNA-b30153/result_gtdb.tsv
[2023-03-16 09:29:29,017] [INFO] ===== GTDB Search completed =====
[2023-03-16 09:29:29,019] [INFO] DFAST_QC result json was written to OceanDNA-b30153/dqc_result.json
[2023-03-16 09:29:29,019] [INFO] DFAST_QC completed!
[2023-03-16 09:29:29,019] [INFO] Total running time: 0h2m32s