[2023-03-17 03:28:37,100] [INFO] DFAST_QC pipeline started.
[2023-03-17 03:28:37,101] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 03:28:37,101] [INFO] DQC Reference Directory: /var/lib/cwl/stgb516387c-2f8d-40da-9b30-5e61d8ccf85c/dqc_reference
[2023-03-17 03:28:38,236] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 03:28:38,236] [INFO] Task started: Prodigal
[2023-03-17 03:28:38,236] [INFO] Running command: cat /var/lib/cwl/stg6f239fa4-0b4e-4a4d-8732-bf6528f6e9b0/OceanDNA-b5753.fa | prodigal -d OceanDNA-b5753/cds.fna -a OceanDNA-b5753/protein.faa -g 11 -q > /dev/null
[2023-03-17 03:28:50,957] [INFO] Task succeeded: Prodigal
[2023-03-17 03:28:50,957] [INFO] Task started: HMMsearch
[2023-03-17 03:28:50,957] [INFO] Running command: hmmsearch --tblout OceanDNA-b5753/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb516387c-2f8d-40da-9b30-5e61d8ccf85c/dqc_reference/reference_markers.hmm OceanDNA-b5753/protein.faa > /dev/null
[2023-03-17 03:28:51,133] [INFO] Task succeeded: HMMsearch
[2023-03-17 03:28:51,133] [INFO] Found 6/6 markers.
[2023-03-17 03:28:51,148] [INFO] Query marker FASTA was written to OceanDNA-b5753/markers.fasta
[2023-03-17 03:28:51,148] [INFO] Task started: Blastn
[2023-03-17 03:28:51,150] [INFO] Running command: blastn -query OceanDNA-b5753/markers.fasta -db /var/lib/cwl/stgb516387c-2f8d-40da-9b30-5e61d8ccf85c/dqc_reference/reference_markers.fasta -out OceanDNA-b5753/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:28:51,684] [INFO] Task succeeded: Blastn
[2023-03-17 03:28:51,686] [INFO] Selected 26 target genomes.
[2023-03-17 03:28:51,686] [INFO] Target genome list was writen to OceanDNA-b5753/target_genomes.txt
[2023-03-17 03:28:51,700] [INFO] Task started: fastANI
[2023-03-17 03:28:51,700] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f239fa4-0b4e-4a4d-8732-bf6528f6e9b0/OceanDNA-b5753.fa --refList OceanDNA-b5753/target_genomes.txt --output OceanDNA-b5753/fastani_result.tsv --threads 1
[2023-03-17 03:29:05,720] [INFO] Task succeeded: fastANI
[2023-03-17 03:29:05,720] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb516387c-2f8d-40da-9b30-5e61d8ccf85c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 03:29:05,720] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb516387c-2f8d-40da-9b30-5e61d8ccf85c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 03:29:05,721] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 03:29:05,721] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 03:29:05,721] [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
--------------------------------------------------------------------------------
[2023-03-17 03:29:05,721] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5753/tc_result.tsv
[2023-03-17 03:29:05,721] [INFO] ===== Taxonomy check completed =====
[2023-03-17 03:29:05,721] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 03:29:05,721] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb516387c-2f8d-40da-9b30-5e61d8ccf85c/dqc_reference/checkm_data
[2023-03-17 03:29:05,724] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 03:29:05,731] [INFO] Task started: CheckM
[2023-03-17 03:29:05,731] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5753/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5753/checkm_input OceanDNA-b5753/checkm_result
[2023-03-17 03:29:41,329] [INFO] Task succeeded: CheckM
[2023-03-17 03:29:41,330] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 03:29:41,332] [INFO] ===== Completeness check finished =====
[2023-03-17 03:29:41,332] [INFO] ===== Start GTDB Search =====
[2023-03-17 03:29:41,332] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5753/markers.fasta)
[2023-03-17 03:29:41,333] [INFO] Task started: Blastn
[2023-03-17 03:29:41,333] [INFO] Running command: blastn -query OceanDNA-b5753/markers.fasta -db /var/lib/cwl/stgb516387c-2f8d-40da-9b30-5e61d8ccf85c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5753/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:29:42,068] [INFO] Task succeeded: Blastn
[2023-03-17 03:29:42,069] [INFO] Selected 15 target genomes.
[2023-03-17 03:29:42,069] [INFO] Target genome list was writen to OceanDNA-b5753/target_genomes_gtdb.txt
[2023-03-17 03:29:42,085] [INFO] Task started: fastANI
[2023-03-17 03:29:42,086] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f239fa4-0b4e-4a4d-8732-bf6528f6e9b0/OceanDNA-b5753.fa --refList OceanDNA-b5753/target_genomes_gtdb.txt --output OceanDNA-b5753/fastani_result_gtdb.tsv --threads 1
[2023-03-17 03:29:49,499] [INFO] Task succeeded: fastANI
[2023-03-17 03:29:49,505] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 03:29:49,505] [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_905478295.1	s__UBA10364 sp002387615	89.5502	473	534	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	99.55	99.11	0.94	0.89	10	-
GCA_018402665.1	s__UBA10364 sp018402665	89.4657	476	534	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	96.42	96.42	0.92	0.92	2	-
GCA_002685435.1	s__UBA10364 sp002685435	86.7164	368	534	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003045825.1	s__UBA10364 sp003045825	82.9423	394	534	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	98.67	96.47	0.88	0.80	20	-
GCA_003385605.1	s__UBA10364 sp003385605	78.5709	131	534	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	99.63	99.63	0.71	0.71	2	-
GCA_012269745.1	s__UBA10364 sp012269745	78.4335	124	534	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018623275.1	s__UBA10364 sp018623275	77.8485	84	534	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003455605.1	s__UBA10364 sp003455605	77.7834	69	534	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 03:29:49,505] [INFO] GTDB search result was written to OceanDNA-b5753/result_gtdb.tsv
[2023-03-17 03:29:49,505] [INFO] ===== GTDB Search completed =====
[2023-03-17 03:29:49,506] [INFO] DFAST_QC result json was written to OceanDNA-b5753/dqc_result.json
[2023-03-17 03:29:49,506] [INFO] DFAST_QC completed!
[2023-03-17 03:29:49,506] [INFO] Total running time: 0h1m12s