[2023-03-19 04:29:37,784] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:29:37,785] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:29:37,785] [INFO] DQC Reference Directory: /var/lib/cwl/stg75dd2acf-dddf-4062-bfcb-2e555bdfa973/dqc_reference
[2023-03-19 04:29:38,891] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:29:38,891] [INFO] Task started: Prodigal
[2023-03-19 04:29:38,891] [INFO] Running command: cat /var/lib/cwl/stg5612b98a-1171-4d28-8c17-4b8e3983b08c/OceanDNA-b8930.fa | prodigal -d OceanDNA-b8930/cds.fna -a OceanDNA-b8930/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:29:45,767] [INFO] Task succeeded: Prodigal
[2023-03-19 04:29:45,767] [INFO] Task started: HMMsearch
[2023-03-19 04:29:45,767] [INFO] Running command: hmmsearch --tblout OceanDNA-b8930/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg75dd2acf-dddf-4062-bfcb-2e555bdfa973/dqc_reference/reference_markers.hmm OceanDNA-b8930/protein.faa > /dev/null
[2023-03-19 04:29:45,956] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:29:45,956] [INFO] Found 6/6 markers.
[2023-03-19 04:29:45,966] [INFO] Query marker FASTA was written to OceanDNA-b8930/markers.fasta
[2023-03-19 04:29:45,966] [INFO] Task started: Blastn
[2023-03-19 04:29:45,967] [INFO] Running command: blastn -query OceanDNA-b8930/markers.fasta -db /var/lib/cwl/stg75dd2acf-dddf-4062-bfcb-2e555bdfa973/dqc_reference/reference_markers.fasta -out OceanDNA-b8930/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:29:46,552] [INFO] Task succeeded: Blastn
[2023-03-19 04:29:46,553] [INFO] Selected 26 target genomes.
[2023-03-19 04:29:46,553] [INFO] Target genome list was writen to OceanDNA-b8930/target_genomes.txt
[2023-03-19 04:29:46,567] [INFO] Task started: fastANI
[2023-03-19 04:29:46,567] [INFO] Running command: fastANI --query /var/lib/cwl/stg5612b98a-1171-4d28-8c17-4b8e3983b08c/OceanDNA-b8930.fa --refList OceanDNA-b8930/target_genomes.txt --output OceanDNA-b8930/fastani_result.tsv --threads 1
[2023-03-19 04:30:01,229] [INFO] Task succeeded: fastANI
[2023-03-19 04:30:01,230] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg75dd2acf-dddf-4062-bfcb-2e555bdfa973/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:30:01,230] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg75dd2acf-dddf-4062-bfcb-2e555bdfa973/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:30:01,230] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:30:01,230] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 04:30:01,230] [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
--------------------------------------------------------------------------------
[2023-03-19 04:30:01,230] [INFO] DFAST Taxonomy check result was written to OceanDNA-b8930/tc_result.tsv
[2023-03-19 04:30:01,230] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:30:01,230] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:30:01,231] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg75dd2acf-dddf-4062-bfcb-2e555bdfa973/dqc_reference/checkm_data
[2023-03-19 04:30:01,233] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:30:01,235] [INFO] Task started: CheckM
[2023-03-19 04:30:01,235] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b8930/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b8930/checkm_input OceanDNA-b8930/checkm_result
[2023-03-19 04:30:23,935] [INFO] Task succeeded: CheckM
[2023-03-19 04:30:23,935] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:30:23,937] [INFO] ===== Completeness check finished =====
[2023-03-19 04:30:23,937] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:30:23,937] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b8930/markers.fasta)
[2023-03-19 04:30:23,937] [INFO] Task started: Blastn
[2023-03-19 04:30:23,937] [INFO] Running command: blastn -query OceanDNA-b8930/markers.fasta -db /var/lib/cwl/stg75dd2acf-dddf-4062-bfcb-2e555bdfa973/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b8930/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:30:24,950] [INFO] Task succeeded: Blastn
[2023-03-19 04:30:24,951] [INFO] Selected 20 target genomes.
[2023-03-19 04:30:24,951] [INFO] Target genome list was writen to OceanDNA-b8930/target_genomes_gtdb.txt
[2023-03-19 04:30:25,025] [INFO] Task started: fastANI
[2023-03-19 04:30:25,025] [INFO] Running command: fastANI --query /var/lib/cwl/stg5612b98a-1171-4d28-8c17-4b8e3983b08c/OceanDNA-b8930.fa --refList OceanDNA-b8930/target_genomes_gtdb.txt --output OceanDNA-b8930/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:30:29,865] [INFO] Task succeeded: fastANI
[2023-03-19 04:30:29,873] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 04:30:29,873] [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_004321735.1	s__MED-G14 sp004321735	98.477	301	373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	96.77	95.40	0.78	0.75	4	conclusive
GCA_002703065.1	s__MED-G14 sp002703065	94.9674	222	373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002457715.1	s__MED-G14 sp002457715	78.1088	102	373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	98.34	98.31	0.91	0.89	3	-
GCA_902554655.1	s__MED-G14 sp902554655	77.8721	122	373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	99.59	99.59	0.62	0.62	2	-
GCA_902520835.1	s__MED-G14 sp902520835	77.7207	153	373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002702385.1	s__MED-G14 sp002702385	77.5278	123	373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002693085.1	s__MED-G14 sp002693085	77.4936	113	373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902574335.1	s__MED-G14 sp902574335	77.1857	50	373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902587325.1	s__MED-G14 sp902587325	77.1475	125	373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	97.53	95.17	0.82	0.78	10	-
GCA_902546095.1	s__MED-G14 sp902546095	76.9539	70	373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902595555.1	s__MED-G14 sp902595555	76.9114	108	373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	96.27	95.29	0.86	0.83	8	-
GCA_902606555.1	s__MED-G14 sp902606555	76.7226	67	373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902622575.1	s__MED-G14 sp902622575	76.7208	79	373	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 04:30:29,873] [INFO] GTDB search result was written to OceanDNA-b8930/result_gtdb.tsv
[2023-03-19 04:30:29,873] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:30:29,874] [INFO] DFAST_QC result json was written to OceanDNA-b8930/dqc_result.json
[2023-03-19 04:30:29,874] [INFO] DFAST_QC completed!
[2023-03-19 04:30:29,874] [INFO] Total running time: 0h0m52s