[2023-03-18 00:35:04,583] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:35:04,583] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:35:04,583] [INFO] DQC Reference Directory: /var/lib/cwl/stg27a3bc22-a818-415a-a6c7-db3c63789c63/dqc_reference
[2023-03-18 00:35:05,659] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:35:05,660] [INFO] Task started: Prodigal
[2023-03-18 00:35:05,660] [INFO] Running command: cat /var/lib/cwl/stg505e8759-7b79-4dbe-8672-aa873f75ec25/OceanDNA-b6335.fa | prodigal -d OceanDNA-b6335/cds.fna -a OceanDNA-b6335/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:35:13,065] [INFO] Task succeeded: Prodigal
[2023-03-18 00:35:13,066] [INFO] Task started: HMMsearch
[2023-03-18 00:35:13,066] [INFO] Running command: hmmsearch --tblout OceanDNA-b6335/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg27a3bc22-a818-415a-a6c7-db3c63789c63/dqc_reference/reference_markers.hmm OceanDNA-b6335/protein.faa > /dev/null
[2023-03-18 00:35:13,256] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:35:13,257] [INFO] Found 6/6 markers.
[2023-03-18 00:35:13,268] [INFO] Query marker FASTA was written to OceanDNA-b6335/markers.fasta
[2023-03-18 00:35:13,268] [INFO] Task started: Blastn
[2023-03-18 00:35:13,268] [INFO] Running command: blastn -query OceanDNA-b6335/markers.fasta -db /var/lib/cwl/stg27a3bc22-a818-415a-a6c7-db3c63789c63/dqc_reference/reference_markers.fasta -out OceanDNA-b6335/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:35:13,874] [INFO] Task succeeded: Blastn
[2023-03-18 00:35:13,875] [INFO] Selected 32 target genomes.
[2023-03-18 00:35:13,875] [INFO] Target genome list was writen to OceanDNA-b6335/target_genomes.txt
[2023-03-18 00:35:13,888] [INFO] Task started: fastANI
[2023-03-18 00:35:13,888] [INFO] Running command: fastANI --query /var/lib/cwl/stg505e8759-7b79-4dbe-8672-aa873f75ec25/OceanDNA-b6335.fa --refList OceanDNA-b6335/target_genomes.txt --output OceanDNA-b6335/fastani_result.tsv --threads 1
[2023-03-18 00:35:31,825] [INFO] Task succeeded: fastANI
[2023-03-18 00:35:31,825] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg27a3bc22-a818-415a-a6c7-db3c63789c63/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:35:31,825] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg27a3bc22-a818-415a-a6c7-db3c63789c63/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:35:31,831] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:35:31,831] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 00:35:31,831] [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
Winogradskyella helgolandensis	strain=Z963	GCA_013404085.1	2697010	2697010	type	True	76.7432	51	401	95	below_threshold
Winogradskyella ludwigii	strain=HL116	GCA_013403985.1	2686076	2686076	type	True	76.4817	50	401	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	76.3433	58	401	95	below_threshold
Aquimarina longa	strain=SW024	GCA_001401755.1	1080221	1080221	type	True	76.3217	50	401	95	below_threshold
Yeosuana marina	strain=JLT21	GCA_011762485.1	1565536	1565536	type	True	76.303	55	401	95	below_threshold
Aquimarina muelleri	strain=KCTC 12285	GCA_014651355.1	279356	279356	type	True	76.0379	50	401	95	below_threshold
Aquimarina muelleri	strain=DSM 19832	GCA_000430665.1	279356	279356	type	True	76.0055	51	401	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 00:35:31,831] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6335/tc_result.tsv
[2023-03-18 00:35:31,831] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:35:31,831] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:35:31,831] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg27a3bc22-a818-415a-a6c7-db3c63789c63/dqc_reference/checkm_data
[2023-03-18 00:35:31,832] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:35:31,835] [INFO] Task started: CheckM
[2023-03-18 00:35:31,835] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6335/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6335/checkm_input OceanDNA-b6335/checkm_result
[2023-03-18 00:35:55,861] [INFO] Task succeeded: CheckM
[2023-03-18 00:35:55,862] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 00:35:55,863] [INFO] ===== Completeness check finished =====
[2023-03-18 00:35:55,864] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:35:55,864] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6335/markers.fasta)
[2023-03-18 00:35:55,864] [INFO] Task started: Blastn
[2023-03-18 00:35:55,864] [INFO] Running command: blastn -query OceanDNA-b6335/markers.fasta -db /var/lib/cwl/stg27a3bc22-a818-415a-a6c7-db3c63789c63/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6335/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:35:56,885] [INFO] Task succeeded: Blastn
[2023-03-18 00:35:56,887] [INFO] Selected 14 target genomes.
[2023-03-18 00:35:56,887] [INFO] Target genome list was writen to OceanDNA-b6335/target_genomes_gtdb.txt
[2023-03-18 00:35:56,910] [INFO] Task started: fastANI
[2023-03-18 00:35:56,910] [INFO] Running command: fastANI --query /var/lib/cwl/stg505e8759-7b79-4dbe-8672-aa873f75ec25/OceanDNA-b6335.fa --refList OceanDNA-b6335/target_genomes_gtdb.txt --output OceanDNA-b6335/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:36:01,690] [INFO] Task succeeded: fastANI
[2023-03-18 00:36:01,695] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 00:36:01,695] [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
GCA_018674025.1	s__SGZJ01 sp018674025	97.5819	291	401	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SGZJ01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902515565.1	s__SGZJ01 sp902515565	94.4466	274	401	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SGZJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004213995.1	s__SGZJ01 sp004213995	89.4627	298	401	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SGZJ01	95.0	95.83	95.53	0.71	0.69	3	-
GCA_905182835.1	s__SGZJ01 sp905182835	79.7749	254	401	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SGZJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008084905.1	s__Xanthomarina maritima	76.6248	53	401	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011777505.1	s__CAU-1491 sp011777505	76.6181	50	401	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__CAU-1491	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002697255.1	s__MED-G13 sp002697255	76.3365	81	401	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 00:36:01,695] [INFO] GTDB search result was written to OceanDNA-b6335/result_gtdb.tsv
[2023-03-18 00:36:01,696] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:36:01,697] [INFO] DFAST_QC result json was written to OceanDNA-b6335/dqc_result.json
[2023-03-18 00:36:01,697] [INFO] DFAST_QC completed!
[2023-03-18 00:36:01,697] [INFO] Total running time: 0h0m57s