[2023-03-16 11:01:17,016] [INFO] DFAST_QC pipeline started.
[2023-03-16 11:01:17,016] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 11:01:17,016] [INFO] DQC Reference Directory: /var/lib/cwl/stge6a2224e-599a-49cf-bb43-fb86ee5c9845/dqc_reference
[2023-03-16 11:01:18,218] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 11:01:18,220] [INFO] Task started: Prodigal
[2023-03-16 11:01:18,220] [INFO] Running command: cat /var/lib/cwl/stg323c3f08-8ace-40b2-aee8-2fe016b7cecf/OceanDNA-b4011.fa | prodigal -d OceanDNA-b4011/cds.fna -a OceanDNA-b4011/protein.faa -g 11 -q > /dev/null
[2023-03-16 11:02:09,240] [INFO] Task succeeded: Prodigal
[2023-03-16 11:02:09,240] [INFO] Task started: HMMsearch
[2023-03-16 11:02:09,241] [INFO] Running command: hmmsearch --tblout OceanDNA-b4011/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge6a2224e-599a-49cf-bb43-fb86ee5c9845/dqc_reference/reference_markers.hmm OceanDNA-b4011/protein.faa > /dev/null
[2023-03-16 11:02:09,480] [INFO] Task succeeded: HMMsearch
[2023-03-16 11:02:09,480] [INFO] Found 6/6 markers.
[2023-03-16 11:02:09,510] [INFO] Query marker FASTA was written to OceanDNA-b4011/markers.fasta
[2023-03-16 11:02:09,511] [INFO] Task started: Blastn
[2023-03-16 11:02:09,511] [INFO] Running command: blastn -query OceanDNA-b4011/markers.fasta -db /var/lib/cwl/stge6a2224e-599a-49cf-bb43-fb86ee5c9845/dqc_reference/reference_markers.fasta -out OceanDNA-b4011/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 11:02:10,042] [INFO] Task succeeded: Blastn
[2023-03-16 11:02:10,043] [INFO] Selected 15 target genomes.
[2023-03-16 11:02:10,043] [INFO] Target genome list was writen to OceanDNA-b4011/target_genomes.txt
[2023-03-16 11:02:10,067] [INFO] Task started: fastANI
[2023-03-16 11:02:10,067] [INFO] Running command: fastANI --query /var/lib/cwl/stg323c3f08-8ace-40b2-aee8-2fe016b7cecf/OceanDNA-b4011.fa --refList OceanDNA-b4011/target_genomes.txt --output OceanDNA-b4011/fastani_result.tsv --threads 1
[2023-03-16 11:02:24,980] [INFO] Task succeeded: fastANI
[2023-03-16 11:02:24,980] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge6a2224e-599a-49cf-bb43-fb86ee5c9845/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 11:02:24,980] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge6a2224e-599a-49cf-bb43-fb86ee5c9845/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 11:02:24,987] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2023-03-16 11:02:24,987] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-16 11:02:24,987] [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
Cyclobacterium amurskyense	strain=KCTC 12363	GCA_001050135.1	320787	320787	type	True	97.7565	1690	1836	95	conclusive
Cyclobacterium qasimii	strain=M12-11B	GCA_000427295.1	1350429	1350429	type	True	83.0309	1312	1836	95	below_threshold
Cyclobacterium qasimii	strain=NBRC 106168	GCA_007991695.1	1350429	1350429	type	True	83.0173	1324	1836	95	below_threshold
Cyclobacterium marinum	strain=DSM 745	GCA_000222485.1	104	104	type	True	82.7595	1060	1836	95	below_threshold
Cyclobacterium jeungdonense	strain=KCTC 23150	GCA_010994275.1	708087	708087	type	True	77.1509	249	1836	95	below_threshold
Cyclobacterium plantarum	strain=GBPx2	GCA_011290685.1	2716263	2716263	type	True	77.1275	304	1836	95	below_threshold
Echinicola marina	strain=SCS 3-6	GCA_020463795.1	2859768	2859768	type	True	76.2579	100	1836	95	below_threshold
Belliella pelovolcani	strain=DSM 46698	GCA_900156785.1	529505	529505	type	True	76.1156	66	1836	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 11:02:24,988] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4011/tc_result.tsv
[2023-03-16 11:02:24,988] [INFO] ===== Taxonomy check completed =====
[2023-03-16 11:02:24,988] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 11:02:24,988] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge6a2224e-599a-49cf-bb43-fb86ee5c9845/dqc_reference/checkm_data
[2023-03-16 11:02:24,989] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 11:02:24,997] [INFO] Task started: CheckM
[2023-03-16 11:02:24,997] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4011/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4011/checkm_input OceanDNA-b4011/checkm_result
[2023-03-16 11:04:21,288] [INFO] Task succeeded: CheckM
[2023-03-16 11:04:21,289] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 11:04:21,294] [INFO] ===== Completeness check finished =====
[2023-03-16 11:04:21,294] [INFO] ===== Start GTDB Search =====
[2023-03-16 11:04:21,294] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4011/markers.fasta)
[2023-03-16 11:04:21,296] [INFO] Task started: Blastn
[2023-03-16 11:04:21,296] [INFO] Running command: blastn -query OceanDNA-b4011/markers.fasta -db /var/lib/cwl/stge6a2224e-599a-49cf-bb43-fb86ee5c9845/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4011/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 11:04:22,205] [INFO] Task succeeded: Blastn
[2023-03-16 11:04:22,206] [INFO] Selected 18 target genomes.
[2023-03-16 11:04:22,206] [INFO] Target genome list was writen to OceanDNA-b4011/target_genomes_gtdb.txt
[2023-03-16 11:04:22,222] [INFO] Task started: fastANI
[2023-03-16 11:04:22,222] [INFO] Running command: fastANI --query /var/lib/cwl/stg323c3f08-8ace-40b2-aee8-2fe016b7cecf/OceanDNA-b4011.fa --refList OceanDNA-b4011/target_genomes_gtdb.txt --output OceanDNA-b4011/fastani_result_gtdb.tsv --threads 1
[2023-03-16 11:04:38,604] [INFO] Task succeeded: fastANI
[2023-03-16 11:04:38,612] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 11:04:38,612] [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_001050135.1	s__Cyclobacterium amurskyense	97.7565	1690	1836	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000427295.1	s__Cyclobacterium qasimii	83.0307	1312	1836	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	99.96	99.96	0.99	0.99	2	-
GCF_000222485.1	s__Cyclobacterium marinum	82.7456	1062	1836	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	98.85	98.76	0.93	0.93	3	-
GCF_010993705.1	s__Cyclobacterium sp010993705	77.4278	278	1836	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010994275.1	s__Cyclobacterium jeungdonense	77.1406	250	1836	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011290685.1	s__Cyclobacterium plantarum	77.1281	304	1836	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007483685.1	s__Litoribacter sp007483685	76.1771	58	1836	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Litoribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156785.1	s__Belliella pelovolcani	76.1156	66	1836	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Belliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018642165.1	s__Echinicola shivajiensis	76.0819	79	1836	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017254845.1	s__Algoriphagus sp017254845	75.8892	84	1836	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015476655.1	s__Aquiflexum lacus	75.8304	72	1836	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Aquiflexum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014838715.1	s__Algoriphagus sp014838715	75.7051	56	1836	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 11:04:38,613] [INFO] GTDB search result was written to OceanDNA-b4011/result_gtdb.tsv
[2023-03-16 11:04:38,614] [INFO] ===== GTDB Search completed =====
[2023-03-16 11:04:38,616] [INFO] DFAST_QC result json was written to OceanDNA-b4011/dqc_result.json
[2023-03-16 11:04:38,617] [INFO] DFAST_QC completed!
[2023-03-16 11:04:38,617] [INFO] Total running time: 0h3m22s