[2023-03-15 21:24:38,437] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:24:38,437] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:24:38,437] [INFO] DQC Reference Directory: /var/lib/cwl/stgb9becd9c-a71a-4c35-82fe-7bc60ce7d9ab/dqc_reference
[2023-03-15 21:24:39,531] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:24:39,531] [INFO] Task started: Prodigal
[2023-03-15 21:24:39,531] [INFO] Running command: cat /var/lib/cwl/stg9809075e-8ee6-473e-bd1d-238d73e3d2b9/OceanDNA-b4494.fa | prodigal -d OceanDNA-b4494/cds.fna -a OceanDNA-b4494/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:25:15,801] [INFO] Task succeeded: Prodigal
[2023-03-15 21:25:15,802] [INFO] Task started: HMMsearch
[2023-03-15 21:25:15,802] [INFO] Running command: hmmsearch --tblout OceanDNA-b4494/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb9becd9c-a71a-4c35-82fe-7bc60ce7d9ab/dqc_reference/reference_markers.hmm OceanDNA-b4494/protein.faa > /dev/null
[2023-03-15 21:25:16,045] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:25:16,045] [INFO] Found 6/6 markers.
[2023-03-15 21:25:16,078] [INFO] Query marker FASTA was written to OceanDNA-b4494/markers.fasta
[2023-03-15 21:25:16,079] [INFO] Task started: Blastn
[2023-03-15 21:25:16,079] [INFO] Running command: blastn -query OceanDNA-b4494/markers.fasta -db /var/lib/cwl/stgb9becd9c-a71a-4c35-82fe-7bc60ce7d9ab/dqc_reference/reference_markers.fasta -out OceanDNA-b4494/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:25:16,610] [INFO] Task succeeded: Blastn
[2023-03-15 21:25:16,611] [INFO] Selected 22 target genomes.
[2023-03-15 21:25:16,611] [INFO] Target genome list was writen to OceanDNA-b4494/target_genomes.txt
[2023-03-15 21:25:16,623] [INFO] Task started: fastANI
[2023-03-15 21:25:16,623] [INFO] Running command: fastANI --query /var/lib/cwl/stg9809075e-8ee6-473e-bd1d-238d73e3d2b9/OceanDNA-b4494.fa --refList OceanDNA-b4494/target_genomes.txt --output OceanDNA-b4494/fastani_result.tsv --threads 1
[2023-03-15 21:25:35,133] [INFO] Task succeeded: fastANI
[2023-03-15 21:25:35,133] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb9becd9c-a71a-4c35-82fe-7bc60ce7d9ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:25:35,134] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb9becd9c-a71a-4c35-82fe-7bc60ce7d9ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:25:35,142] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:25:35,142] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 21:25:35,142] [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
Dyadobacter jejuensis	strain=DSM 100346	GCA_003149085.1	1082580	1082580	type	True	78.0216	202	1661	95	below_threshold
Dyadobacter crusticola	strain=DSM 16708	GCA_000701505.1	292407	292407	type	True	77.327	97	1661	95	below_threshold
Dyadobacter koreensis	strain=DSM 19938	GCA_900108855.1	408657	408657	type	True	77.1119	127	1661	95	below_threshold
Dyadobacter sediminis	strain=CGMCC 1.12895	GCA_014640015.1	1493691	1493691	type	True	77.0873	106	1661	95	below_threshold
Dyadobacter luticola	strain=T17	GCA_005860805.1	1979387	1979387	type	True	77.0607	109	1661	95	below_threshold
Dyadobacter psychrophilus	strain=DSM 22270	GCA_900167945.1	651661	651661	type	True	77.0422	117	1661	95	below_threshold
Dyadobacter bucti	strain=QTA69	GCA_005869225.1	2572203	2572203	type	True	77.0076	121	1661	95	below_threshold
Dyadobacter endophyticus	strain=CGMCC 1.15288	GCA_014641595.1	1749036	1749036	type	True	76.9814	91	1661	95	below_threshold
Dyadobacter alkalitolerans	strain=DSM 23607	GCA_000428845.1	492736	492736	type	True	76.8305	122	1661	95	below_threshold
Dyadobacter subterraneus	strain=UP-52	GCA_015221875.1	2773304	2773304	type	True	76.8192	138	1661	95	below_threshold
Dyadobacter arcticus	strain=DSM 102865	GCA_011762185.1	1078754	1078754	type	True	76.5209	99	1661	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 21:25:35,142] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4494/tc_result.tsv
[2023-03-15 21:25:35,142] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:25:35,142] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:25:35,142] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb9becd9c-a71a-4c35-82fe-7bc60ce7d9ab/dqc_reference/checkm_data
[2023-03-15 21:25:35,143] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:25:35,153] [INFO] Task started: CheckM
[2023-03-15 21:25:35,153] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4494/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4494/checkm_input OceanDNA-b4494/checkm_result
[2023-03-15 21:27:03,037] [INFO] Task succeeded: CheckM
[2023-03-15 21:27:03,037] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 21:27:03,041] [INFO] ===== Completeness check finished =====
[2023-03-15 21:27:03,041] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:27:03,041] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4494/markers.fasta)
[2023-03-15 21:27:03,042] [INFO] Task started: Blastn
[2023-03-15 21:27:03,042] [INFO] Running command: blastn -query OceanDNA-b4494/markers.fasta -db /var/lib/cwl/stgb9becd9c-a71a-4c35-82fe-7bc60ce7d9ab/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4494/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:27:03,762] [INFO] Task succeeded: Blastn
[2023-03-15 21:27:03,763] [INFO] Selected 29 target genomes.
[2023-03-15 21:27:03,763] [INFO] Target genome list was writen to OceanDNA-b4494/target_genomes_gtdb.txt
[2023-03-15 21:27:04,384] [INFO] Task started: fastANI
[2023-03-15 21:27:04,384] [INFO] Running command: fastANI --query /var/lib/cwl/stg9809075e-8ee6-473e-bd1d-238d73e3d2b9/OceanDNA-b4494.fa --refList OceanDNA-b4494/target_genomes_gtdb.txt --output OceanDNA-b4494/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:27:28,948] [INFO] Task succeeded: fastANI
[2023-03-15 21:27:28,957] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 21:27:28,957] [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_003149085.1	s__Dyadobacter jejuensis	78.0216	202	1661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_907164905.1	s__Dyadobacter sp907164905	77.6555	147	1661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000701505.1	s__Dyadobacter crusticola	77.327	97	1661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_907165045.1	s__Dyadobacter sp907165045	77.2169	119	1661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424405.1	s__Dyadobacter sp001424405	77.1198	96	1661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108855.1	s__Dyadobacter koreensis	77.1119	127	1661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005860805.1	s__Dyadobacter luticola	77.0607	109	1661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005860765.1	s__Dyadobacter sediminis	77.0138	104	1661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005869225.1	s__Dyadobacter bucti	77.0076	121	1661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009801115.1	s__Dyadobacter sp009801115	76.9776	155	1661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008369915.1	s__Dyadobacter sp008369915	76.8574	97	1661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015221875.1	s__Dyadobacter sp015221875	76.8192	138	1661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005280585.1	s__Dyadobacter frigoris	76.7348	157	1661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011762185.1	s__Dyadobacter arcticus	76.5209	99	1661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 21:27:28,957] [INFO] GTDB search result was written to OceanDNA-b4494/result_gtdb.tsv
[2023-03-15 21:27:28,957] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:27:28,959] [INFO] DFAST_QC result json was written to OceanDNA-b4494/dqc_result.json
[2023-03-15 21:27:28,959] [INFO] DFAST_QC completed!
[2023-03-15 21:27:28,959] [INFO] Total running time: 0h2m51s