[2023-03-18 00:21:54,216] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:21:54,216] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:21:54,216] [INFO] DQC Reference Directory: /var/lib/cwl/stg3298b184-cf32-470e-a467-9099fe211c7d/dqc_reference
[2023-03-18 00:21:55,650] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:21:55,651] [INFO] Task started: Prodigal
[2023-03-18 00:21:55,651] [INFO] Running command: cat /var/lib/cwl/stg88c07129-7a1f-493e-a570-48ed5c499eaf/OceanDNA-b11904.fa | prodigal -d OceanDNA-b11904/cds.fna -a OceanDNA-b11904/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:22:08,850] [INFO] Task succeeded: Prodigal
[2023-03-18 00:22:08,850] [INFO] Task started: HMMsearch
[2023-03-18 00:22:08,850] [INFO] Running command: hmmsearch --tblout OceanDNA-b11904/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3298b184-cf32-470e-a467-9099fe211c7d/dqc_reference/reference_markers.hmm OceanDNA-b11904/protein.faa > /dev/null
[2023-03-18 00:22:08,991] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:22:08,992] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg88c07129-7a1f-493e-a570-48ed5c499eaf/OceanDNA-b11904.fa]
[2023-03-18 00:22:09,003] [INFO] Query marker FASTA was written to OceanDNA-b11904/markers.fasta
[2023-03-18 00:22:09,003] [INFO] Task started: Blastn
[2023-03-18 00:22:09,004] [INFO] Running command: blastn -query OceanDNA-b11904/markers.fasta -db /var/lib/cwl/stg3298b184-cf32-470e-a467-9099fe211c7d/dqc_reference/reference_markers.fasta -out OceanDNA-b11904/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:22:09,519] [INFO] Task succeeded: Blastn
[2023-03-18 00:22:09,520] [INFO] Selected 23 target genomes.
[2023-03-18 00:22:09,520] [INFO] Target genome list was writen to OceanDNA-b11904/target_genomes.txt
[2023-03-18 00:22:09,531] [INFO] Task started: fastANI
[2023-03-18 00:22:09,531] [INFO] Running command: fastANI --query /var/lib/cwl/stg88c07129-7a1f-493e-a570-48ed5c499eaf/OceanDNA-b11904.fa --refList OceanDNA-b11904/target_genomes.txt --output OceanDNA-b11904/fastani_result.tsv --threads 1
[2023-03-18 00:22:25,528] [INFO] Task succeeded: fastANI
[2023-03-18 00:22:25,529] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3298b184-cf32-470e-a467-9099fe211c7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:22:25,529] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3298b184-cf32-470e-a467-9099fe211c7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:22:25,529] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:22:25,529] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 00:22:25,529] [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
--------------------------------------------------------------------------------
[2023-03-18 00:22:25,529] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11904/tc_result.tsv
[2023-03-18 00:22:25,529] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:22:25,530] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:22:25,530] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3298b184-cf32-470e-a467-9099fe211c7d/dqc_reference/checkm_data
[2023-03-18 00:22:25,532] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:22:25,536] [INFO] Task started: CheckM
[2023-03-18 00:22:25,537] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11904/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11904/checkm_input OceanDNA-b11904/checkm_result
[2023-03-18 00:23:00,569] [INFO] Task succeeded: CheckM
[2023-03-18 00:23:00,569] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.89%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:23:00,571] [INFO] ===== Completeness check finished =====
[2023-03-18 00:23:00,571] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:23:00,571] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11904/markers.fasta)
[2023-03-18 00:23:00,572] [INFO] Task started: Blastn
[2023-03-18 00:23:00,572] [INFO] Running command: blastn -query OceanDNA-b11904/markers.fasta -db /var/lib/cwl/stg3298b184-cf32-470e-a467-9099fe211c7d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11904/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:23:01,265] [INFO] Task succeeded: Blastn
[2023-03-18 00:23:01,266] [INFO] Selected 11 target genomes.
[2023-03-18 00:23:01,266] [INFO] Target genome list was writen to OceanDNA-b11904/target_genomes_gtdb.txt
[2023-03-18 00:23:01,275] [INFO] Task started: fastANI
[2023-03-18 00:23:01,275] [INFO] Running command: fastANI --query /var/lib/cwl/stg88c07129-7a1f-493e-a570-48ed5c499eaf/OceanDNA-b11904.fa --refList OceanDNA-b11904/target_genomes_gtdb.txt --output OceanDNA-b11904/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:23:05,904] [INFO] Task succeeded: fastANI
[2023-03-18 00:23:05,908] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 00:23:05,908] [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_002729115.1	s__UBA11663 sp002729115	90.6455	157	201	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA11663	95.0	96.51	95.05	0.71	0.69	4	-
GCA_002469765.1	s__UBA11663 sp002469765	84.0946	174	201	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA11663	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002683345.1	s__UBA11663 sp002683345	78.5955	77	201	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA11663	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011524845.1	s__UBA11663 sp011524845	78.3445	86	201	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA11663	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002863145.1	s__UBA11663 sp002863145	78.3368	89	201	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA11663	95.0	97.56	96.60	0.84	0.82	6	-
--------------------------------------------------------------------------------
[2023-03-18 00:23:05,908] [INFO] GTDB search result was written to OceanDNA-b11904/result_gtdb.tsv
[2023-03-18 00:23:05,909] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:23:05,909] [INFO] DFAST_QC result json was written to OceanDNA-b11904/dqc_result.json
[2023-03-18 00:23:05,909] [INFO] DFAST_QC completed!
[2023-03-18 00:23:05,909] [INFO] Total running time: 0h1m12s