[2023-03-18 02:27:37,198] [INFO] DFAST_QC pipeline started.
[2023-03-18 02:27:37,198] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 02:27:37,198] [INFO] DQC Reference Directory: /var/lib/cwl/stgcb904986-9a35-46a2-af9b-2527a7c33caa/dqc_reference
[2023-03-18 02:27:38,489] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 02:27:38,489] [INFO] Task started: Prodigal
[2023-03-18 02:27:38,489] [INFO] Running command: cat /var/lib/cwl/stg9fca5a2a-abe6-4f3f-8225-6fc555c15474/OceanDNA-b10098.fa | prodigal -d OceanDNA-b10098/cds.fna -a OceanDNA-b10098/protein.faa -g 11 -q > /dev/null
[2023-03-18 02:27:56,938] [INFO] Task succeeded: Prodigal
[2023-03-18 02:27:56,939] [INFO] Task started: HMMsearch
[2023-03-18 02:27:56,939] [INFO] Running command: hmmsearch --tblout OceanDNA-b10098/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcb904986-9a35-46a2-af9b-2527a7c33caa/dqc_reference/reference_markers.hmm OceanDNA-b10098/protein.faa > /dev/null
[2023-03-18 02:27:57,184] [INFO] Task succeeded: HMMsearch
[2023-03-18 02:27:57,184] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9fca5a2a-abe6-4f3f-8225-6fc555c15474/OceanDNA-b10098.fa]
[2023-03-18 02:27:57,204] [INFO] Query marker FASTA was written to OceanDNA-b10098/markers.fasta
[2023-03-18 02:27:57,204] [INFO] Task started: Blastn
[2023-03-18 02:27:57,204] [INFO] Running command: blastn -query OceanDNA-b10098/markers.fasta -db /var/lib/cwl/stgcb904986-9a35-46a2-af9b-2527a7c33caa/dqc_reference/reference_markers.fasta -out OceanDNA-b10098/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:27:57,788] [INFO] Task succeeded: Blastn
[2023-03-18 02:27:57,789] [INFO] Selected 17 target genomes.
[2023-03-18 02:27:57,789] [INFO] Target genome list was writen to OceanDNA-b10098/target_genomes.txt
[2023-03-18 02:27:57,796] [INFO] Task started: fastANI
[2023-03-18 02:27:57,796] [INFO] Running command: fastANI --query /var/lib/cwl/stg9fca5a2a-abe6-4f3f-8225-6fc555c15474/OceanDNA-b10098.fa --refList OceanDNA-b10098/target_genomes.txt --output OceanDNA-b10098/fastani_result.tsv --threads 1
[2023-03-18 02:28:09,785] [INFO] Task succeeded: fastANI
[2023-03-18 02:28:09,786] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcb904986-9a35-46a2-af9b-2527a7c33caa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:28:09,786] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcb904986-9a35-46a2-af9b-2527a7c33caa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:28:09,792] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 02:28:09,792] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 02:28:09,792] [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
Robiginitalea biformata	strain=HTCC2501	GCA_000024125.1	252307	252307	type	True	98.9936	634	660	95	conclusive
Robiginitalea sediminis	strain=O458	GCA_002198115.1	1982593	1982593	type	True	77.9158	237	660	95	below_threshold
Robiginitalea myxolifaciens	strain=DSM 21019	GCA_900115205.1	400055	400055	type	True	76.339	110	660	95	below_threshold
Muriicola marianensis	strain=CGMCC 1.12606	GCA_014638095.1	1324801	1324801	type	True	76.3322	83	660	95	below_threshold
Zeaxanthinibacter enoshimensis	strain=DSM 18435	GCA_004362865.1	392009	392009	type	True	76.2053	71	660	95	below_threshold
Muriicola jejuensis	strain=KCTC 22299	GCA_010671595.1	504488	504488	type	True	76.0684	91	660	95	below_threshold
Muricauda hadalis	strain=MT-229	GCA_007785775.2	2597517	2597517	type	True	75.7398	52	660	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 02:28:09,792] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10098/tc_result.tsv
[2023-03-18 02:28:09,792] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:28:09,792] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:28:09,792] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcb904986-9a35-46a2-af9b-2527a7c33caa/dqc_reference/checkm_data
[2023-03-18 02:28:09,793] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:28:09,808] [INFO] Task started: CheckM
[2023-03-18 02:28:09,808] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10098/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10098/checkm_input OceanDNA-b10098/checkm_result
[2023-03-18 02:28:57,399] [INFO] Task succeeded: CheckM
[2023-03-18 02:28:57,399] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 02:28:57,402] [INFO] ===== Completeness check finished =====
[2023-03-18 02:28:57,402] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:28:57,402] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10098/markers.fasta)
[2023-03-18 02:28:57,402] [INFO] Task started: Blastn
[2023-03-18 02:28:57,402] [INFO] Running command: blastn -query OceanDNA-b10098/markers.fasta -db /var/lib/cwl/stgcb904986-9a35-46a2-af9b-2527a7c33caa/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10098/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:28:58,328] [INFO] Task succeeded: Blastn
[2023-03-18 02:28:58,328] [INFO] Selected 11 target genomes.
[2023-03-18 02:28:58,329] [INFO] Target genome list was writen to OceanDNA-b10098/target_genomes_gtdb.txt
[2023-03-18 02:28:58,337] [INFO] Task started: fastANI
[2023-03-18 02:28:58,337] [INFO] Running command: fastANI --query /var/lib/cwl/stg9fca5a2a-abe6-4f3f-8225-6fc555c15474/OceanDNA-b10098.fa --refList OceanDNA-b10098/target_genomes_gtdb.txt --output OceanDNA-b10098/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:29:04,977] [INFO] Task succeeded: fastANI
[2023-03-18 02:29:04,982] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 02:29:04,983] [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_000024125.1	s__Robiginitalea biformata	98.9936	634	660	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Robiginitalea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014243345.1	s__Robiginitalea sp014243345	80.0984	420	660	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Robiginitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002198115.1	s__Robiginitalea sediminis	77.9158	237	660	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Robiginitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006227965.1	s__Robiginitalea sp006227965	76.737	84	660	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Robiginitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115205.1	s__Robiginitalea myxolifaciens	76.3555	109	660	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Robiginitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014638095.1	s__Muriicola marianensis	76.3322	83	660	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muriicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001683825.1	s__Zeaxanthinibacter sp001683825	76.0949	122	660	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zeaxanthinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010671595.1	s__Muriicola jejuensis	76.0684	91	660	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muriicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 02:29:04,983] [INFO] GTDB search result was written to OceanDNA-b10098/result_gtdb.tsv
[2023-03-18 02:29:04,983] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:29:04,984] [INFO] DFAST_QC result json was written to OceanDNA-b10098/dqc_result.json
[2023-03-18 02:29:04,984] [INFO] DFAST_QC completed!
[2023-03-18 02:29:04,984] [INFO] Total running time: 0h1m28s