[2023-03-16 17:59:31,146] [INFO] DFAST_QC pipeline started.
[2023-03-16 17:59:31,146] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 17:59:31,147] [INFO] DQC Reference Directory: /var/lib/cwl/stg3e592875-511c-4a85-9bb5-f947eff8816d/dqc_reference
[2023-03-16 17:59:32,478] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 17:59:32,482] [INFO] Task started: Prodigal
[2023-03-16 17:59:32,483] [INFO] Running command: cat /var/lib/cwl/stg525048fd-6b4d-4da2-853d-bbf8964fc30e/OceanDNA-b5316.fa | prodigal -d OceanDNA-b5316/cds.fna -a OceanDNA-b5316/protein.faa -g 11 -q > /dev/null
[2023-03-16 17:59:59,727] [INFO] Task succeeded: Prodigal
[2023-03-16 17:59:59,727] [INFO] Task started: HMMsearch
[2023-03-16 17:59:59,727] [INFO] Running command: hmmsearch --tblout OceanDNA-b5316/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3e592875-511c-4a85-9bb5-f947eff8816d/dqc_reference/reference_markers.hmm OceanDNA-b5316/protein.faa > /dev/null
[2023-03-16 17:59:59,900] [INFO] Task succeeded: HMMsearch
[2023-03-16 17:59:59,901] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg525048fd-6b4d-4da2-853d-bbf8964fc30e/OceanDNA-b5316.fa]
[2023-03-16 17:59:59,920] [INFO] Query marker FASTA was written to OceanDNA-b5316/markers.fasta
[2023-03-16 17:59:59,921] [INFO] Task started: Blastn
[2023-03-16 17:59:59,921] [INFO] Running command: blastn -query OceanDNA-b5316/markers.fasta -db /var/lib/cwl/stg3e592875-511c-4a85-9bb5-f947eff8816d/dqc_reference/reference_markers.fasta -out OceanDNA-b5316/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:00:00,412] [INFO] Task succeeded: Blastn
[2023-03-16 18:00:00,413] [INFO] Selected 15 target genomes.
[2023-03-16 18:00:00,413] [INFO] Target genome list was writen to OceanDNA-b5316/target_genomes.txt
[2023-03-16 18:00:00,418] [INFO] Task started: fastANI
[2023-03-16 18:00:00,418] [INFO] Running command: fastANI --query /var/lib/cwl/stg525048fd-6b4d-4da2-853d-bbf8964fc30e/OceanDNA-b5316.fa --refList OceanDNA-b5316/target_genomes.txt --output OceanDNA-b5316/fastani_result.tsv --threads 1
[2023-03-16 18:00:08,568] [INFO] Task succeeded: fastANI
[2023-03-16 18:00:08,568] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3e592875-511c-4a85-9bb5-f947eff8816d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 18:00:08,568] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3e592875-511c-4a85-9bb5-f947eff8816d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 18:00:08,569] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 18:00:08,569] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 18:00:08,569] [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
--------------------------------------------------------------------------------
[2023-03-16 18:00:08,569] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5316/tc_result.tsv
[2023-03-16 18:00:08,569] [INFO] ===== Taxonomy check completed =====
[2023-03-16 18:00:08,569] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 18:00:08,569] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3e592875-511c-4a85-9bb5-f947eff8816d/dqc_reference/checkm_data
[2023-03-16 18:00:08,579] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 18:00:08,817] [INFO] Task started: CheckM
[2023-03-16 18:00:08,817] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5316/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5316/checkm_input OceanDNA-b5316/checkm_result
[2023-03-16 18:01:17,288] [INFO] Task succeeded: CheckM
[2023-03-16 18:01:17,289] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 5.15%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 18:01:17,292] [INFO] ===== Completeness check finished =====
[2023-03-16 18:01:17,292] [INFO] ===== Start GTDB Search =====
[2023-03-16 18:01:17,293] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5316/markers.fasta)
[2023-03-16 18:01:17,294] [INFO] Task started: Blastn
[2023-03-16 18:01:17,294] [INFO] Running command: blastn -query OceanDNA-b5316/markers.fasta -db /var/lib/cwl/stg3e592875-511c-4a85-9bb5-f947eff8816d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5316/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:01:17,882] [INFO] Task succeeded: Blastn
[2023-03-16 18:01:17,885] [INFO] Selected 20 target genomes.
[2023-03-16 18:01:17,885] [INFO] Target genome list was writen to OceanDNA-b5316/target_genomes_gtdb.txt
[2023-03-16 18:01:18,004] [INFO] Task started: fastANI
[2023-03-16 18:01:18,004] [INFO] Running command: fastANI --query /var/lib/cwl/stg525048fd-6b4d-4da2-853d-bbf8964fc30e/OceanDNA-b5316.fa --refList OceanDNA-b5316/target_genomes_gtdb.txt --output OceanDNA-b5316/fastani_result_gtdb.tsv --threads 1
[2023-03-16 18:01:29,963] [INFO] Task succeeded: fastANI
[2023-03-16 18:01:29,968] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 18:01:29,968] [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_002733985.1	s__UBA4466 sp002733985	78.3053	316	850	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	96.56	96.56	0.90	0.90	2	-
GCA_013373595.1	s__UBA4466 sp013373595	77.6814	244	850	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002471375.1	s__UBA4466 sp002471375	76.8536	62	850	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002734065.2	s__UBA4466 sp002734065	76.747	60	850	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015665275.1	s__UBA4466 sp015665275	76.683	59	850	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903945495.1	s__M0103 sp903945495	76.6332	81	850	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__M0103	95.0	99.87	99.80	0.95	0.92	6	-
GCA_017984635.1	s__M0103 sp017984635	76.586	53	850	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__M0103	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003149635.1	s__UBA4466 sp003149635	76.4969	83	850	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 18:01:29,969] [INFO] GTDB search result was written to OceanDNA-b5316/result_gtdb.tsv
[2023-03-16 18:01:29,970] [INFO] ===== GTDB Search completed =====
[2023-03-16 18:01:29,971] [INFO] DFAST_QC result json was written to OceanDNA-b5316/dqc_result.json
[2023-03-16 18:01:29,971] [INFO] DFAST_QC completed!
[2023-03-16 18:01:29,971] [INFO] Total running time: 0h1m59s