[2023-03-18 03:27:00,414] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:27:00,414] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:27:00,414] [INFO] DQC Reference Directory: /var/lib/cwl/stgd6156bee-38c3-4c5c-96ce-674eeeff5ba0/dqc_reference
[2023-03-18 03:27:01,575] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:27:01,576] [INFO] Task started: Prodigal
[2023-03-18 03:27:01,576] [INFO] Running command: cat /var/lib/cwl/stgb2bef6c0-ce95-4f3b-b018-3d80e91b22c7/OceanDNA-b30139.fa | prodigal -d OceanDNA-b30139/cds.fna -a OceanDNA-b30139/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:27:10,185] [INFO] Task succeeded: Prodigal
[2023-03-18 03:27:10,185] [INFO] Task started: HMMsearch
[2023-03-18 03:27:10,185] [INFO] Running command: hmmsearch --tblout OceanDNA-b30139/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd6156bee-38c3-4c5c-96ce-674eeeff5ba0/dqc_reference/reference_markers.hmm OceanDNA-b30139/protein.faa > /dev/null
[2023-03-18 03:27:10,338] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:27:10,338] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgb2bef6c0-ce95-4f3b-b018-3d80e91b22c7/OceanDNA-b30139.fa]
[2023-03-18 03:27:10,359] [INFO] Query marker FASTA was written to OceanDNA-b30139/markers.fasta
[2023-03-18 03:27:10,360] [INFO] Task started: Blastn
[2023-03-18 03:27:10,360] [INFO] Running command: blastn -query OceanDNA-b30139/markers.fasta -db /var/lib/cwl/stgd6156bee-38c3-4c5c-96ce-674eeeff5ba0/dqc_reference/reference_markers.fasta -out OceanDNA-b30139/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:27:11,085] [INFO] Task succeeded: Blastn
[2023-03-18 03:27:11,086] [INFO] Selected 14 target genomes.
[2023-03-18 03:27:11,086] [INFO] Target genome list was writen to OceanDNA-b30139/target_genomes.txt
[2023-03-18 03:27:11,094] [INFO] Task started: fastANI
[2023-03-18 03:27:11,094] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2bef6c0-ce95-4f3b-b018-3d80e91b22c7/OceanDNA-b30139.fa --refList OceanDNA-b30139/target_genomes.txt --output OceanDNA-b30139/fastani_result.tsv --threads 1
[2023-03-18 03:27:20,081] [INFO] Task succeeded: fastANI
[2023-03-18 03:27:20,081] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd6156bee-38c3-4c5c-96ce-674eeeff5ba0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:27:20,081] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd6156bee-38c3-4c5c-96ce-674eeeff5ba0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:27:20,089] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 03:27:20,089] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 03:27:20,089] [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 bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	98.0923	145	161	95	conclusive
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	84.1638	119	161	95	below_threshold
Salipiger profundus	strain=JLT2016	GCA_001969385.1	1229727	1229727	type	True	83.5263	118	161	95	below_threshold
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	83.3601	118	161	95	below_threshold
Yangia pacifica	strain=CGMCC 1.3455	GCA_900100725.1	311180	311180	suspected-type	True	82.2221	103	161	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	82.1368	105	161	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	80.9857	99	161	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	79.6819	93	161	95	below_threshold
Mameliella sediminis	strain=DP3N28-2	GCA_019218285.1	2836866	2836866	type	True	78.9072	56	161	95	below_threshold
Roseivivax jejudonensis	strain=CECT 8625	GCA_900172265.1	1529041	1529041	type	True	78.8263	67	161	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.287	51	161	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 03:27:20,089] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30139/tc_result.tsv
[2023-03-18 03:27:20,089] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:27:20,089] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:27:20,089] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd6156bee-38c3-4c5c-96ce-674eeeff5ba0/dqc_reference/checkm_data
[2023-03-18 03:27:20,090] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:27:20,094] [INFO] Task started: CheckM
[2023-03-18 03:27:20,094] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30139/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30139/checkm_input OceanDNA-b30139/checkm_result
[2023-03-18 03:27:46,430] [INFO] Task succeeded: CheckM
[2023-03-18 03:27:46,431] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.28%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 03:27:46,433] [INFO] ===== Completeness check finished =====
[2023-03-18 03:27:46,433] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:27:46,433] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30139/markers.fasta)
[2023-03-18 03:27:46,434] [INFO] Task started: Blastn
[2023-03-18 03:27:46,434] [INFO] Running command: blastn -query OceanDNA-b30139/markers.fasta -db /var/lib/cwl/stgd6156bee-38c3-4c5c-96ce-674eeeff5ba0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30139/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:27:47,668] [INFO] Task succeeded: Blastn
[2023-03-18 03:27:47,668] [INFO] Selected 10 target genomes.
[2023-03-18 03:27:47,668] [INFO] Target genome list was writen to OceanDNA-b30139/target_genomes_gtdb.txt
[2023-03-18 03:27:47,676] [INFO] Task started: fastANI
[2023-03-18 03:27:47,676] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2bef6c0-ce95-4f3b-b018-3d80e91b22c7/OceanDNA-b30139.fa --refList OceanDNA-b30139/target_genomes_gtdb.txt --output OceanDNA-b30139/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:27:55,401] [INFO] Task succeeded: fastANI
[2023-03-18 03:27:55,408] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 03:27:55,408] [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_000153725.1	s__Salipiger bermudensis	98.0923	145	161	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.06	97.75	0.87	0.75	4	conclusive
GCF_900102075.1	s__Salipiger thiooxidans	84.1638	119	161	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.34	95.88	0.90	0.85	6	-
GCF_001969385.1	s__Salipiger profundus	83.4506	119	161	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	99.85	99.64	0.97	0.94	5	-
GCF_001975705.1	s__Salipiger abyssi	83.1121	109	161	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017311415.1	s__Salipiger abyssi_A	82.4999	110	161	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116195.1	s__Salipiger pacificus	82.1368	105	161	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000442255.1	s__Salipiger mucosus	82.1055	94	161	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001687105.1	s__Salipiger sp001687105	81.2023	101	161	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	96.47	96.47	0.82	0.82	2	-
GCF_014643635.1	s__Salipiger pallidus	80.9857	99	161	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	80.7357	102	161	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 03:27:55,408] [INFO] GTDB search result was written to OceanDNA-b30139/result_gtdb.tsv
[2023-03-18 03:27:55,408] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:27:55,409] [INFO] DFAST_QC result json was written to OceanDNA-b30139/dqc_result.json
[2023-03-18 03:27:55,409] [INFO] DFAST_QC completed!
[2023-03-18 03:27:55,410] [INFO] Total running time: 0h0m55s