[2023-03-15 11:20:29,270] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:20:29,271] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:20:29,271] [INFO] DQC Reference Directory: /var/lib/cwl/stge4ee116a-616c-45c4-8231-7fbc72492b67/dqc_reference
[2023-03-15 11:20:30,349] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:20:30,350] [INFO] Task started: Prodigal
[2023-03-15 11:20:30,350] [INFO] Running command: cat /var/lib/cwl/stg7ef9e2e9-51cd-4340-9b87-2461dc9a767e/OceanDNA-b35196.fa | prodigal -d OceanDNA-b35196/cds.fna -a OceanDNA-b35196/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:20:47,907] [INFO] Task succeeded: Prodigal
[2023-03-15 11:20:47,908] [INFO] Task started: HMMsearch
[2023-03-15 11:20:47,908] [INFO] Running command: hmmsearch --tblout OceanDNA-b35196/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge4ee116a-616c-45c4-8231-7fbc72492b67/dqc_reference/reference_markers.hmm OceanDNA-b35196/protein.faa > /dev/null
[2023-03-15 11:20:48,129] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:20:48,129] [INFO] Found 6/6 markers.
[2023-03-15 11:20:48,177] [INFO] Query marker FASTA was written to OceanDNA-b35196/markers.fasta
[2023-03-15 11:20:48,179] [INFO] Task started: Blastn
[2023-03-15 11:20:48,179] [INFO] Running command: blastn -query OceanDNA-b35196/markers.fasta -db /var/lib/cwl/stge4ee116a-616c-45c4-8231-7fbc72492b67/dqc_reference/reference_markers.fasta -out OceanDNA-b35196/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:20:48,829] [INFO] Task succeeded: Blastn
[2023-03-15 11:20:48,833] [INFO] Selected 34 target genomes.
[2023-03-15 11:20:48,833] [INFO] Target genome list was writen to OceanDNA-b35196/target_genomes.txt
[2023-03-15 11:20:48,857] [INFO] Task started: fastANI
[2023-03-15 11:20:48,857] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ef9e2e9-51cd-4340-9b87-2461dc9a767e/OceanDNA-b35196.fa --refList OceanDNA-b35196/target_genomes.txt --output OceanDNA-b35196/fastani_result.tsv --threads 1
[2023-03-15 11:21:12,317] [INFO] Task succeeded: fastANI
[2023-03-15 11:21:12,317] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge4ee116a-616c-45c4-8231-7fbc72492b67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:21:12,317] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge4ee116a-616c-45c4-8231-7fbc72492b67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:21:12,321] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:21:12,322] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 11:21:12,322] [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
Shewanella vesiculosa	strain=M7	GCA_021560015.1	518738	518738	type	True	76.0063	52	1066	95	below_threshold
Shewanella vesiculosa	strain=LMG 24424	GCA_003797885.1	518738	518738	type	True	75.9735	51	1066	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 11:21:12,323] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35196/tc_result.tsv
[2023-03-15 11:21:12,326] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:21:12,326] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:21:12,326] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge4ee116a-616c-45c4-8231-7fbc72492b67/dqc_reference/checkm_data
[2023-03-15 11:21:12,327] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:21:12,335] [INFO] Task started: CheckM
[2023-03-15 11:21:12,335] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35196/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35196/checkm_input OceanDNA-b35196/checkm_result
[2023-03-15 11:21:57,661] [INFO] Task succeeded: CheckM
[2023-03-15 11:21:57,661] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:21:57,740] [INFO] ===== Completeness check finished =====
[2023-03-15 11:21:57,740] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:21:57,740] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35196/markers.fasta)
[2023-03-15 11:21:57,742] [INFO] Task started: Blastn
[2023-03-15 11:21:57,742] [INFO] Running command: blastn -query OceanDNA-b35196/markers.fasta -db /var/lib/cwl/stge4ee116a-616c-45c4-8231-7fbc72492b67/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35196/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:21:58,703] [INFO] Task succeeded: Blastn
[2023-03-15 11:21:58,719] [INFO] Selected 19 target genomes.
[2023-03-15 11:21:58,719] [INFO] Target genome list was writen to OceanDNA-b35196/target_genomes_gtdb.txt
[2023-03-15 11:21:58,732] [INFO] Task started: fastANI
[2023-03-15 11:21:58,732] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ef9e2e9-51cd-4340-9b87-2461dc9a767e/OceanDNA-b35196.fa --refList OceanDNA-b35196/target_genomes_gtdb.txt --output OceanDNA-b35196/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:22:11,357] [INFO] Task succeeded: fastANI
[2023-03-15 11:22:11,363] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 11:22:11,363] [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_013214905.1	s__Psychrobium sp013214905	92.8475	743	1066	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychrobiaceae;g__Psychrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214965.1	s__Psychrobium sp013214965	78.3825	187	1066	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychrobiaceae;g__Psychrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214885.1	s__Psychrobium sp013214885	78.364	139	1066	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychrobiaceae;g__Psychrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214945.1	s__Psychrobium sp013214945	78.1658	154	1066	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychrobiaceae;g__Psychrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002835545.1	s__Psychrobium sp002835545	78.1155	147	1066	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychrobiaceae;g__Psychrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001874365.1	s__Psychrobium sp001874365	77.2744	118	1066	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychrobiaceae;g__Psychrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214175.1	s__Colwellia sp013214175	76.3799	60	1066	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	95.17	95.17	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-03-15 11:22:11,364] [INFO] GTDB search result was written to OceanDNA-b35196/result_gtdb.tsv
[2023-03-15 11:22:11,366] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:22:11,369] [INFO] DFAST_QC result json was written to OceanDNA-b35196/dqc_result.json
[2023-03-15 11:22:11,369] [INFO] DFAST_QC completed!
[2023-03-15 11:22:11,369] [INFO] Total running time: 0h1m42s