[2023-03-18 08:36:16,001] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:36:16,001] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:36:16,001] [INFO] DQC Reference Directory: /var/lib/cwl/stg52366562-67b4-4ebe-bb8c-7ea3a4c2a83b/dqc_reference
[2023-03-18 08:36:17,822] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:36:17,823] [INFO] Task started: Prodigal
[2023-03-18 08:36:17,823] [INFO] Running command: cat /var/lib/cwl/stg4431119e-3602-4fc8-820f-70e5ef36a69f/OceanDNA-b39304.fa | prodigal -d OceanDNA-b39304/cds.fna -a OceanDNA-b39304/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:36:33,197] [INFO] Task succeeded: Prodigal
[2023-03-18 08:36:33,197] [INFO] Task started: HMMsearch
[2023-03-18 08:36:33,197] [INFO] Running command: hmmsearch --tblout OceanDNA-b39304/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg52366562-67b4-4ebe-bb8c-7ea3a4c2a83b/dqc_reference/reference_markers.hmm OceanDNA-b39304/protein.faa > /dev/null
[2023-03-18 08:36:33,393] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:36:33,394] [INFO] Found 6/6 markers.
[2023-03-18 08:36:33,413] [INFO] Query marker FASTA was written to OceanDNA-b39304/markers.fasta
[2023-03-18 08:36:33,414] [INFO] Task started: Blastn
[2023-03-18 08:36:33,415] [INFO] Running command: blastn -query OceanDNA-b39304/markers.fasta -db /var/lib/cwl/stg52366562-67b4-4ebe-bb8c-7ea3a4c2a83b/dqc_reference/reference_markers.fasta -out OceanDNA-b39304/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:36:33,999] [INFO] Task succeeded: Blastn
[2023-03-18 08:36:34,000] [INFO] Selected 25 target genomes.
[2023-03-18 08:36:34,000] [INFO] Target genome list was writen to OceanDNA-b39304/target_genomes.txt
[2023-03-18 08:36:34,033] [INFO] Task started: fastANI
[2023-03-18 08:36:34,033] [INFO] Running command: fastANI --query /var/lib/cwl/stg4431119e-3602-4fc8-820f-70e5ef36a69f/OceanDNA-b39304.fa --refList OceanDNA-b39304/target_genomes.txt --output OceanDNA-b39304/fastani_result.tsv --threads 1
[2023-03-18 08:36:49,673] [INFO] Task succeeded: fastANI
[2023-03-18 08:36:49,673] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg52366562-67b4-4ebe-bb8c-7ea3a4c2a83b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:36:49,673] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg52366562-67b4-4ebe-bb8c-7ea3a4c2a83b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:36:49,673] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:36:49,674] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 08:36:49,674] [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 08:36:49,694] [INFO] DFAST Taxonomy check result was written to OceanDNA-b39304/tc_result.tsv
[2023-03-18 08:36:49,722] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:36:49,722] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:36:49,722] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg52366562-67b4-4ebe-bb8c-7ea3a4c2a83b/dqc_reference/checkm_data
[2023-03-18 08:36:49,725] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:36:49,730] [INFO] Task started: CheckM
[2023-03-18 08:36:49,730] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b39304/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b39304/checkm_input OceanDNA-b39304/checkm_result
[2023-03-18 08:37:30,600] [INFO] Task succeeded: CheckM
[2023-03-18 08:37:30,601] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 08:37:30,608] [INFO] ===== Completeness check finished =====
[2023-03-18 08:37:30,608] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:37:30,608] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b39304/markers.fasta)
[2023-03-18 08:37:30,609] [INFO] Task started: Blastn
[2023-03-18 08:37:30,610] [INFO] Running command: blastn -query OceanDNA-b39304/markers.fasta -db /var/lib/cwl/stg52366562-67b4-4ebe-bb8c-7ea3a4c2a83b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b39304/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:37:31,545] [INFO] Task succeeded: Blastn
[2023-03-18 08:37:31,547] [INFO] Selected 32 target genomes.
[2023-03-18 08:37:31,547] [INFO] Target genome list was writen to OceanDNA-b39304/target_genomes_gtdb.txt
[2023-03-18 08:37:31,592] [INFO] Task started: fastANI
[2023-03-18 08:37:31,592] [INFO] Running command: fastANI --query /var/lib/cwl/stg4431119e-3602-4fc8-820f-70e5ef36a69f/OceanDNA-b39304.fa --refList OceanDNA-b39304/target_genomes_gtdb.txt --output OceanDNA-b39304/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:37:48,668] [INFO] Task succeeded: fastANI
[2023-03-18 08:37:48,672] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 08:37:48,672] [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_003645535.1	s__HB2-32-21 sp003645535	76.7627	108	850	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HB2-32-21	95.0	99.14	99.14	0.68	0.68	2	-
GCA_018069465.1	s__50-400-T64 sp018069465	76.7279	90	850	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__50-400-T64	95.0	100.00	100.00	0.99	0.99	2	-
GCA_002162755.1	s__50-400-T64 sp002162755	76.1628	54	850	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__50-400-T64	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002162815.1	s__50-400-T64 sp002162815	76.1478	54	850	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__50-400-T64	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 08:37:48,673] [INFO] GTDB search result was written to OceanDNA-b39304/result_gtdb.tsv
[2023-03-18 08:37:48,673] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:37:48,675] [INFO] DFAST_QC result json was written to OceanDNA-b39304/dqc_result.json
[2023-03-18 08:37:48,675] [INFO] DFAST_QC completed!
[2023-03-18 08:37:48,675] [INFO] Total running time: 0h1m33s