[2023-03-16 09:01:44,907] [INFO] DFAST_QC pipeline started.
[2023-03-16 09:01:44,907] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 09:01:44,907] [INFO] DQC Reference Directory: /var/lib/cwl/stge25a858d-d009-434a-800e-5874bacef23b/dqc_reference
[2023-03-16 09:01:46,034] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 09:01:46,035] [INFO] Task started: Prodigal
[2023-03-16 09:01:46,035] [INFO] Running command: cat /var/lib/cwl/stg415d033a-111b-4755-867b-cf3078f7ac55/OceanDNA-b10914.fa | prodigal -d OceanDNA-b10914/cds.fna -a OceanDNA-b10914/protein.faa -g 11 -q > /dev/null
[2023-03-16 09:01:58,624] [INFO] Task succeeded: Prodigal
[2023-03-16 09:01:58,625] [INFO] Task started: HMMsearch
[2023-03-16 09:01:58,625] [INFO] Running command: hmmsearch --tblout OceanDNA-b10914/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge25a858d-d009-434a-800e-5874bacef23b/dqc_reference/reference_markers.hmm OceanDNA-b10914/protein.faa > /dev/null
[2023-03-16 09:01:58,806] [INFO] Task succeeded: HMMsearch
[2023-03-16 09:01:58,807] [INFO] Found 6/6 markers.
[2023-03-16 09:01:58,820] [INFO] Query marker FASTA was written to OceanDNA-b10914/markers.fasta
[2023-03-16 09:01:58,825] [INFO] Task started: Blastn
[2023-03-16 09:01:58,825] [INFO] Running command: blastn -query OceanDNA-b10914/markers.fasta -db /var/lib/cwl/stge25a858d-d009-434a-800e-5874bacef23b/dqc_reference/reference_markers.fasta -out OceanDNA-b10914/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:01:59,428] [INFO] Task succeeded: Blastn
[2023-03-16 09:01:59,428] [INFO] Selected 32 target genomes.
[2023-03-16 09:01:59,429] [INFO] Target genome list was writen to OceanDNA-b10914/target_genomes.txt
[2023-03-16 09:01:59,470] [INFO] Task started: fastANI
[2023-03-16 09:01:59,470] [INFO] Running command: fastANI --query /var/lib/cwl/stg415d033a-111b-4755-867b-cf3078f7ac55/OceanDNA-b10914.fa --refList OceanDNA-b10914/target_genomes.txt --output OceanDNA-b10914/fastani_result.tsv --threads 1
[2023-03-16 09:02:16,087] [INFO] Task succeeded: fastANI
[2023-03-16 09:02:16,088] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge25a858d-d009-434a-800e-5874bacef23b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 09:02:16,088] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge25a858d-d009-434a-800e-5874bacef23b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 09:02:16,088] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 09:02:16,088] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 09:02:16,088] [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 09:02:16,088] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10914/tc_result.tsv
[2023-03-16 09:02:16,088] [INFO] ===== Taxonomy check completed =====
[2023-03-16 09:02:16,089] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 09:02:16,089] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge25a858d-d009-434a-800e-5874bacef23b/dqc_reference/checkm_data
[2023-03-16 09:02:16,092] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 09:02:16,099] [INFO] Task started: CheckM
[2023-03-16 09:02:16,099] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10914/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10914/checkm_input OceanDNA-b10914/checkm_result
[2023-03-16 09:02:50,719] [INFO] Task succeeded: CheckM
[2023-03-16 09:02:50,719] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 09:02:50,722] [INFO] ===== Completeness check finished =====
[2023-03-16 09:02:50,723] [INFO] ===== Start GTDB Search =====
[2023-03-16 09:02:50,723] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10914/markers.fasta)
[2023-03-16 09:02:50,724] [INFO] Task started: Blastn
[2023-03-16 09:02:50,724] [INFO] Running command: blastn -query OceanDNA-b10914/markers.fasta -db /var/lib/cwl/stge25a858d-d009-434a-800e-5874bacef23b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10914/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:02:51,504] [INFO] Task succeeded: Blastn
[2023-03-16 09:02:51,506] [INFO] Selected 20 target genomes.
[2023-03-16 09:02:51,506] [INFO] Target genome list was writen to OceanDNA-b10914/target_genomes_gtdb.txt
[2023-03-16 09:02:51,658] [INFO] Task started: fastANI
[2023-03-16 09:02:51,658] [INFO] Running command: fastANI --query /var/lib/cwl/stg415d033a-111b-4755-867b-cf3078f7ac55/OceanDNA-b10914.fa --refList OceanDNA-b10914/target_genomes_gtdb.txt --output OceanDNA-b10914/fastani_result_gtdb.tsv --threads 1
[2023-03-16 09:02:58,891] [INFO] Task succeeded: fastANI
[2023-03-16 09:02:58,898] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 09:02:58,898] [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_011526275.1	s__UBA7428 sp011526275	77.9386	168	617	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478905.1	s__UBA7428 sp905478905	77.9128	162	617	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	98.97	98.97	0.80	0.80	2	-
GCA_011526285.1	s__UBA7428 sp011526285	77.7197	168	617	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003023645.1	s__UBA7428 sp003023645	77.4451	76	617	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	99.50	99.50	0.87	0.87	2	-
GCA_002477625.1	s__UBA7428 sp002477625	77.1114	68	617	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	98.28	97.25	0.74	0.68	4	-
GCA_018608425.1	s__UBA7428 sp018608425	77.0931	65	617	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011526335.1	s__UBA7428 sp011526335	77.0324	92	617	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181615.1	s__UBA7428 sp905181615	76.8051	83	617	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	99.59	99.59	0.98	0.98	2	-
GCA_017852075.1	s__MS024-2A sp017852075	76.4335	54	617	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	99.70	99.69	0.95	0.94	3	-
GCA_002708445.1	s__UBA7428 sp002708445	76.1748	61	617	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 09:02:58,899] [INFO] GTDB search result was written to OceanDNA-b10914/result_gtdb.tsv
[2023-03-16 09:02:58,900] [INFO] ===== GTDB Search completed =====
[2023-03-16 09:02:58,901] [INFO] DFAST_QC result json was written to OceanDNA-b10914/dqc_result.json
[2023-03-16 09:02:58,902] [INFO] DFAST_QC completed!
[2023-03-16 09:02:58,902] [INFO] Total running time: 0h1m14s