[2023-03-16 22:05:57,080] [INFO] DFAST_QC pipeline started.
[2023-03-16 22:05:57,080] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 22:05:57,080] [INFO] DQC Reference Directory: /var/lib/cwl/stgd55ed269-ec67-4b03-877c-0867d9629e9d/dqc_reference
[2023-03-16 22:05:58,247] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 22:05:58,248] [INFO] Task started: Prodigal
[2023-03-16 22:05:58,248] [INFO] Running command: cat /var/lib/cwl/stge98fd432-545d-451d-b6e6-4d1aa968b696/OceanDNA-b12885.fa | prodigal -d OceanDNA-b12885/cds.fna -a OceanDNA-b12885/protein.faa -g 11 -q > /dev/null
[2023-03-16 22:06:10,674] [INFO] Task succeeded: Prodigal
[2023-03-16 22:06:10,674] [INFO] Task started: HMMsearch
[2023-03-16 22:06:10,674] [INFO] Running command: hmmsearch --tblout OceanDNA-b12885/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd55ed269-ec67-4b03-877c-0867d9629e9d/dqc_reference/reference_markers.hmm OceanDNA-b12885/protein.faa > /dev/null
[2023-03-16 22:06:10,865] [INFO] Task succeeded: HMMsearch
[2023-03-16 22:06:10,865] [WARNING] Found 3/6 markers. [/var/lib/cwl/stge98fd432-545d-451d-b6e6-4d1aa968b696/OceanDNA-b12885.fa]
[2023-03-16 22:06:10,890] [INFO] Query marker FASTA was written to OceanDNA-b12885/markers.fasta
[2023-03-16 22:06:10,890] [INFO] Task started: Blastn
[2023-03-16 22:06:10,891] [INFO] Running command: blastn -query OceanDNA-b12885/markers.fasta -db /var/lib/cwl/stgd55ed269-ec67-4b03-877c-0867d9629e9d/dqc_reference/reference_markers.fasta -out OceanDNA-b12885/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 22:06:11,378] [INFO] Task succeeded: Blastn
[2023-03-16 22:06:11,379] [INFO] Selected 15 target genomes.
[2023-03-16 22:06:11,379] [INFO] Target genome list was writen to OceanDNA-b12885/target_genomes.txt
[2023-03-16 22:06:11,388] [INFO] Task started: fastANI
[2023-03-16 22:06:11,388] [INFO] Running command: fastANI --query /var/lib/cwl/stge98fd432-545d-451d-b6e6-4d1aa968b696/OceanDNA-b12885.fa --refList OceanDNA-b12885/target_genomes.txt --output OceanDNA-b12885/fastani_result.tsv --threads 1
[2023-03-16 22:06:20,222] [INFO] Task succeeded: fastANI
[2023-03-16 22:06:20,222] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd55ed269-ec67-4b03-877c-0867d9629e9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 22:06:20,223] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd55ed269-ec67-4b03-877c-0867d9629e9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 22:06:20,223] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 22:06:20,223] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 22:06:20,223] [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 22:06:20,223] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12885/tc_result.tsv
[2023-03-16 22:06:20,223] [INFO] ===== Taxonomy check completed =====
[2023-03-16 22:06:20,223] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 22:06:20,223] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd55ed269-ec67-4b03-877c-0867d9629e9d/dqc_reference/checkm_data
[2023-03-16 22:06:20,226] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 22:06:20,231] [INFO] Task started: CheckM
[2023-03-16 22:06:20,231] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12885/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12885/checkm_input OceanDNA-b12885/checkm_result
[2023-03-16 22:06:55,392] [INFO] Task succeeded: CheckM
[2023-03-16 22:06:55,393] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.49%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 22:06:55,395] [INFO] ===== Completeness check finished =====
[2023-03-16 22:06:55,395] [INFO] ===== Start GTDB Search =====
[2023-03-16 22:06:55,396] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12885/markers.fasta)
[2023-03-16 22:06:55,397] [INFO] Task started: Blastn
[2023-03-16 22:06:55,397] [INFO] Running command: blastn -query OceanDNA-b12885/markers.fasta -db /var/lib/cwl/stgd55ed269-ec67-4b03-877c-0867d9629e9d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12885/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 22:06:56,064] [INFO] Task succeeded: Blastn
[2023-03-16 22:06:56,065] [INFO] Selected 13 target genomes.
[2023-03-16 22:06:56,065] [INFO] Target genome list was writen to OceanDNA-b12885/target_genomes_gtdb.txt
[2023-03-16 22:06:56,549] [INFO] Task started: fastANI
[2023-03-16 22:06:56,549] [INFO] Running command: fastANI --query /var/lib/cwl/stge98fd432-545d-451d-b6e6-4d1aa968b696/OceanDNA-b12885.fa --refList OceanDNA-b12885/target_genomes_gtdb.txt --output OceanDNA-b12885/fastani_result_gtdb.tsv --threads 1
[2023-03-16 22:07:03,922] [INFO] Task succeeded: fastANI
[2023-03-16 22:07:03,925] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 22:07:03,925] [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_013112585.1	s__IGN16 sp013112585	80.9895	425	713	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Melioribacteraceae;g__IGN16	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002698995.1	s__GCA-2698995 sp002698995	76.3189	55	713	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Melioribacteraceae;g__GCA-2698995	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016708125.1	s__GCA-2746605 sp016708125	75.3932	70	713	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__Ignavibacteriales;f__Melioribacteraceae;g__GCA-2746605	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 22:07:03,925] [INFO] GTDB search result was written to OceanDNA-b12885/result_gtdb.tsv
[2023-03-16 22:07:03,926] [INFO] ===== GTDB Search completed =====
[2023-03-16 22:07:03,926] [INFO] DFAST_QC result json was written to OceanDNA-b12885/dqc_result.json
[2023-03-16 22:07:03,926] [INFO] DFAST_QC completed!
[2023-03-16 22:07:03,926] [INFO] Total running time: 0h1m7s