[2023-03-18 10:16:27,290] [INFO] DFAST_QC pipeline started.
[2023-03-18 10:16:27,290] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 10:16:27,290] [INFO] DQC Reference Directory: /var/lib/cwl/stgaa4a0a59-6c37-4fb1-8836-2e8e877a25cf/dqc_reference
[2023-03-18 10:16:28,367] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 10:16:28,368] [INFO] Task started: Prodigal
[2023-03-18 10:16:28,368] [INFO] Running command: cat /var/lib/cwl/stgc5e6430e-abac-479d-b3ff-ce650cae4126/OceanDNA-b34896.fa | prodigal -d OceanDNA-b34896/cds.fna -a OceanDNA-b34896/protein.faa -g 11 -q > /dev/null
[2023-03-18 10:16:52,859] [INFO] Task succeeded: Prodigal
[2023-03-18 10:16:52,859] [INFO] Task started: HMMsearch
[2023-03-18 10:16:52,859] [INFO] Running command: hmmsearch --tblout OceanDNA-b34896/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaa4a0a59-6c37-4fb1-8836-2e8e877a25cf/dqc_reference/reference_markers.hmm OceanDNA-b34896/protein.faa > /dev/null
[2023-03-18 10:16:53,067] [INFO] Task succeeded: HMMsearch
[2023-03-18 10:16:53,068] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgc5e6430e-abac-479d-b3ff-ce650cae4126/OceanDNA-b34896.fa]
[2023-03-18 10:16:53,110] [INFO] Query marker FASTA was written to OceanDNA-b34896/markers.fasta
[2023-03-18 10:16:53,111] [INFO] Task started: Blastn
[2023-03-18 10:16:53,111] [INFO] Running command: blastn -query OceanDNA-b34896/markers.fasta -db /var/lib/cwl/stgaa4a0a59-6c37-4fb1-8836-2e8e877a25cf/dqc_reference/reference_markers.fasta -out OceanDNA-b34896/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:16:53,561] [INFO] Task succeeded: Blastn
[2023-03-18 10:16:53,566] [INFO] Selected 16 target genomes.
[2023-03-18 10:16:53,566] [INFO] Target genome list was writen to OceanDNA-b34896/target_genomes.txt
[2023-03-18 10:16:53,576] [INFO] Task started: fastANI
[2023-03-18 10:16:53,576] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5e6430e-abac-479d-b3ff-ce650cae4126/OceanDNA-b34896.fa --refList OceanDNA-b34896/target_genomes.txt --output OceanDNA-b34896/fastani_result.tsv --threads 1
[2023-03-18 10:17:05,732] [INFO] Task succeeded: fastANI
[2023-03-18 10:17:05,732] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaa4a0a59-6c37-4fb1-8836-2e8e877a25cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 10:17:05,732] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaa4a0a59-6c37-4fb1-8836-2e8e877a25cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 10:17:05,738] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 10:17:05,738] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 10:17:05,738] [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
Paraglaciecola arctica	strain=BSs20135	GCA_000314995.1	1128911	1128911	type	True	82.6389	947	1479	95	below_threshold
Paraglaciecola psychrophila	strain=170	GCA_000347635.1	326544	326544	type	True	80.03	665	1479	95	below_threshold
Paraglaciecola psychrophila	strain=170	GCA_000315075.1	326544	326544	type	True	80.0097	672	1479	95	below_threshold
Paraglaciecola marina	strain=D3211	GCA_004360155.1	2500157	2500157	type	True	78.3019	249	1479	95	below_threshold
Paraglaciecola aquimarina	strain=GGW-M5	GCA_021532655.1	1235557	1235557	type	True	78.1116	241	1479	95	below_threshold
Paraglaciecola polaris	strain=LMG 21857	GCA_000315055.1	222814	222814	type	True	77.0687	133	1479	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 10:17:05,738] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34896/tc_result.tsv
[2023-03-18 10:17:05,739] [INFO] ===== Taxonomy check completed =====
[2023-03-18 10:17:05,739] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 10:17:05,739] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaa4a0a59-6c37-4fb1-8836-2e8e877a25cf/dqc_reference/checkm_data
[2023-03-18 10:17:05,740] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 10:17:05,747] [INFO] Task started: CheckM
[2023-03-18 10:17:05,747] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34896/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34896/checkm_input OceanDNA-b34896/checkm_result
[2023-03-18 10:18:06,091] [INFO] Task succeeded: CheckM
[2023-03-18 10:18:06,091] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 10:18:06,120] [INFO] ===== Completeness check finished =====
[2023-03-18 10:18:06,120] [INFO] ===== Start GTDB Search =====
[2023-03-18 10:18:06,120] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34896/markers.fasta)
[2023-03-18 10:18:06,122] [INFO] Task started: Blastn
[2023-03-18 10:18:06,122] [INFO] Running command: blastn -query OceanDNA-b34896/markers.fasta -db /var/lib/cwl/stgaa4a0a59-6c37-4fb1-8836-2e8e877a25cf/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34896/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:18:06,561] [INFO] Task succeeded: Blastn
[2023-03-18 10:18:06,573] [INFO] Selected 7 target genomes.
[2023-03-18 10:18:06,573] [INFO] Target genome list was writen to OceanDNA-b34896/target_genomes_gtdb.txt
[2023-03-18 10:18:06,612] [INFO] Task started: fastANI
[2023-03-18 10:18:06,612] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5e6430e-abac-479d-b3ff-ce650cae4126/OceanDNA-b34896.fa --refList OceanDNA-b34896/target_genomes_gtdb.txt --output OceanDNA-b34896/fastani_result_gtdb.tsv --threads 1
[2023-03-18 10:18:13,442] [INFO] Task succeeded: fastANI
[2023-03-18 10:18:13,448] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 10:18:13,448] [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
GCF_000314995.1	s__Paraglaciecola arctica	82.6272	948	1479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018861065.1	s__Paraglaciecola arctica_B	82.1363	886	1479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003232445.1	s__Paraglaciecola arctica_A	81.4261	403	1479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002835935.1	s__Paraglaciecola sp002835935	80.5653	729	1479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000347635.1	s__Paraglaciecola psychrophila	80.03	665	1479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	99.98	99.98	1.00	1.00	2	-
GCA_905479025.1	s__Paraglaciecola sp905479025	79.5274	313	1479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000315055.1	s__Paraglaciecola polaris	77.0687	133	1479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 10:18:13,453] [INFO] GTDB search result was written to OceanDNA-b34896/result_gtdb.tsv
[2023-03-18 10:18:13,460] [INFO] ===== GTDB Search completed =====
[2023-03-18 10:18:13,464] [INFO] DFAST_QC result json was written to OceanDNA-b34896/dqc_result.json
[2023-03-18 10:18:13,464] [INFO] DFAST_QC completed!
[2023-03-18 10:18:13,464] [INFO] Total running time: 0h1m46s