[2023-03-16 10:35:17,642] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:35:17,642] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:35:17,642] [INFO] DQC Reference Directory: /var/lib/cwl/stgc2385507-4864-4953-9051-7f6042147975/dqc_reference
[2023-03-16 10:35:18,829] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:35:18,830] [INFO] Task started: Prodigal
[2023-03-16 10:35:18,830] [INFO] Running command: cat /var/lib/cwl/stgec5081cf-444f-4f94-80f0-9125c8de36d0/OceanDNA-b14404.fa | prodigal -d OceanDNA-b14404/cds.fna -a OceanDNA-b14404/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:35:33,894] [INFO] Task succeeded: Prodigal
[2023-03-16 10:35:33,895] [INFO] Task started: HMMsearch
[2023-03-16 10:35:33,895] [INFO] Running command: hmmsearch --tblout OceanDNA-b14404/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc2385507-4864-4953-9051-7f6042147975/dqc_reference/reference_markers.hmm OceanDNA-b14404/protein.faa > /dev/null
[2023-03-16 10:35:34,124] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:35:34,125] [INFO] Found 6/6 markers.
[2023-03-16 10:35:34,141] [INFO] Query marker FASTA was written to OceanDNA-b14404/markers.fasta
[2023-03-16 10:35:34,144] [INFO] Task started: Blastn
[2023-03-16 10:35:34,144] [INFO] Running command: blastn -query OceanDNA-b14404/markers.fasta -db /var/lib/cwl/stgc2385507-4864-4953-9051-7f6042147975/dqc_reference/reference_markers.fasta -out OceanDNA-b14404/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:35:34,734] [INFO] Task succeeded: Blastn
[2023-03-16 10:35:34,735] [INFO] Selected 15 target genomes.
[2023-03-16 10:35:34,735] [INFO] Target genome list was writen to OceanDNA-b14404/target_genomes.txt
[2023-03-16 10:35:34,742] [INFO] Task started: fastANI
[2023-03-16 10:35:34,742] [INFO] Running command: fastANI --query /var/lib/cwl/stgec5081cf-444f-4f94-80f0-9125c8de36d0/OceanDNA-b14404.fa --refList OceanDNA-b14404/target_genomes.txt --output OceanDNA-b14404/fastani_result.tsv --threads 1
[2023-03-16 10:35:45,245] [INFO] Task succeeded: fastANI
[2023-03-16 10:35:45,245] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc2385507-4864-4953-9051-7f6042147975/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:35:45,246] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc2385507-4864-4953-9051-7f6042147975/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:35:45,246] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:35:45,246] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 10:35:45,246] [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 10:35:45,246] [INFO] DFAST Taxonomy check result was written to OceanDNA-b14404/tc_result.tsv
[2023-03-16 10:35:45,246] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:35:45,246] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:35:45,246] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc2385507-4864-4953-9051-7f6042147975/dqc_reference/checkm_data
[2023-03-16 10:35:45,249] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:35:45,253] [INFO] Task started: CheckM
[2023-03-16 10:35:45,253] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b14404/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b14404/checkm_input OceanDNA-b14404/checkm_result
[2023-03-16 10:36:24,438] [INFO] Task succeeded: CheckM
[2023-03-16 10:36:24,439] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 10:36:24,441] [INFO] ===== Completeness check finished =====
[2023-03-16 10:36:24,441] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:36:24,441] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b14404/markers.fasta)
[2023-03-16 10:36:24,443] [INFO] Task started: Blastn
[2023-03-16 10:36:24,443] [INFO] Running command: blastn -query OceanDNA-b14404/markers.fasta -db /var/lib/cwl/stgc2385507-4864-4953-9051-7f6042147975/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b14404/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:36:25,183] [INFO] Task succeeded: Blastn
[2023-03-16 10:36:25,184] [INFO] Selected 21 target genomes.
[2023-03-16 10:36:25,185] [INFO] Target genome list was writen to OceanDNA-b14404/target_genomes_gtdb.txt
[2023-03-16 10:36:25,220] [INFO] Task started: fastANI
[2023-03-16 10:36:25,220] [INFO] Running command: fastANI --query /var/lib/cwl/stgec5081cf-444f-4f94-80f0-9125c8de36d0/OceanDNA-b14404.fa --refList OceanDNA-b14404/target_genomes_gtdb.txt --output OceanDNA-b14404/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:36:35,438] [INFO] Task succeeded: fastANI
[2023-03-16 10:36:35,445] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 10:36:35,445] [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_018650845.1	s__UBA1328 sp018650845	76.7856	125	740	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__UBA1328	95.0	99.74	99.74	0.93	0.93	2	-
GCA_012959765.1	s__UBA1328 sp012959765	76.661	98	740	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__UBA1328	95.0	99.88	99.88	0.97	0.97	2	-
GCA_018649665.1	s__UBA1328 sp018649665	76.4131	96	740	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__UBA1328	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002313245.1	s__UBA9455 sp002313245	76.2492	61	740	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__UBA9455	95.0	97.93	97.22	0.78	0.67	5	-
GCA_013204545.1	s__UBA1328 sp013204545	76.1055	77	740	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__UBA1328	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 10:36:35,446] [INFO] GTDB search result was written to OceanDNA-b14404/result_gtdb.tsv
[2023-03-16 10:36:35,446] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:36:35,448] [INFO] DFAST_QC result json was written to OceanDNA-b14404/dqc_result.json
[2023-03-16 10:36:35,448] [INFO] DFAST_QC completed!
[2023-03-16 10:36:35,448] [INFO] Total running time: 0h1m18s