[2023-03-19 04:11:06,923] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:11:06,923] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:11:06,923] [INFO] DQC Reference Directory: /var/lib/cwl/stg965c00a2-60b6-41c5-99d0-c0c4e52c37dd/dqc_reference
[2023-03-19 04:11:08,557] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:11:08,557] [INFO] Task started: Prodigal
[2023-03-19 04:11:08,557] [INFO] Running command: cat /var/lib/cwl/stgd9ce63ca-84bc-4c0a-a3e7-5c15be836c3c/OceanDNA-b7470.fa | prodigal -d OceanDNA-b7470/cds.fna -a OceanDNA-b7470/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:11:26,213] [INFO] Task succeeded: Prodigal
[2023-03-19 04:11:26,214] [INFO] Task started: HMMsearch
[2023-03-19 04:11:26,214] [INFO] Running command: hmmsearch --tblout OceanDNA-b7470/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg965c00a2-60b6-41c5-99d0-c0c4e52c37dd/dqc_reference/reference_markers.hmm OceanDNA-b7470/protein.faa > /dev/null
[2023-03-19 04:11:26,426] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:11:26,427] [INFO] Found 6/6 markers.
[2023-03-19 04:11:26,445] [INFO] Query marker FASTA was written to OceanDNA-b7470/markers.fasta
[2023-03-19 04:11:26,445] [INFO] Task started: Blastn
[2023-03-19 04:11:26,445] [INFO] Running command: blastn -query OceanDNA-b7470/markers.fasta -db /var/lib/cwl/stg965c00a2-60b6-41c5-99d0-c0c4e52c37dd/dqc_reference/reference_markers.fasta -out OceanDNA-b7470/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:11:27,083] [INFO] Task succeeded: Blastn
[2023-03-19 04:11:27,084] [INFO] Selected 21 target genomes.
[2023-03-19 04:11:27,085] [INFO] Target genome list was writen to OceanDNA-b7470/target_genomes.txt
[2023-03-19 04:11:27,095] [INFO] Task started: fastANI
[2023-03-19 04:11:27,095] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9ce63ca-84bc-4c0a-a3e7-5c15be836c3c/OceanDNA-b7470.fa --refList OceanDNA-b7470/target_genomes.txt --output OceanDNA-b7470/fastani_result.tsv --threads 1
[2023-03-19 04:11:40,646] [INFO] Task succeeded: fastANI
[2023-03-19 04:11:40,647] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg965c00a2-60b6-41c5-99d0-c0c4e52c37dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:11:40,647] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg965c00a2-60b6-41c5-99d0-c0c4e52c37dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:11:40,658] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:11:40,658] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 04:11:40,659] [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
Lacinutrix algicola	strain=AKS293	GCA_001418085.1	342954	342954	type	True	80.6742	604	1011	95	below_threshold
Lacinutrix mariniflava	strain=AKS432	GCA_001418015.1	342955	342955	type	True	80.1311	632	1011	95	below_threshold
Lacinutrix jangbogonensis	strain=PAMC 27137	GCA_000797445.1	1469557	1469557	type	True	79.7509	520	1011	95	below_threshold
Olleya aquimaris	strain=DSM 24464	GCA_003259525.1	639310	639310	type	True	78.9176	446	1011	95	below_threshold
Olleya namhaensis	strain=DSM 28881	GCA_900114005.1	1144750	1144750	type	True	78.8989	451	1011	95	below_threshold
Mesoflavibacter zeaxanthinifaciens	strain=DSM 18436	GCA_000422365.1	393060	393060	type	True	78.8055	471	1011	95	below_threshold
Mesoflavibacter zeaxanthinifaciens subsp. sabulilitoris	strain=CECT 8597	GCA_014191595.1	1520893	393060	type	True	78.7743	459	1011	95	below_threshold
Mesoflavibacter zeaxanthinifaciens subsp. sabulilitoris	strain=KCTC 42117	GCA_003008435.1	1520893	393060	type	True	78.7296	459	1011	95	below_threshold
Mesoflavibacter profundi	strain=YC1039	GCA_014764305.1	2708110	2708110	type	True	78.6708	469	1011	95	below_threshold
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	78.6227	447	1011	95	below_threshold
Oceanihabitans sediminis	strain=S9-10	GCA_003337215.1	1812012	1812012	type	True	78.2165	307	1011	95	below_threshold
Bizionia paragorgiae	strain=DSM 23842	GCA_900107625.1	283786	283786	type	True	78.2052	315	1011	95	below_threshold
Oceanihabitans sediminis	strain=DSM 28133	GCA_003315315.1	1812012	1812012	type	True	78.2032	305	1011	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	78.1867	299	1011	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	78.0305	336	1011	95	below_threshold
Winogradskyella eckloniae	strain=EC29	GCA_013249045.1	1089306	1089306	type	True	77.9849	313	1011	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	77.6209	288	1011	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	77.4164	230	1011	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	77.1933	265	1011	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	77.1849	202	1011	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	76.9938	249	1011	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 04:11:40,659] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7470/tc_result.tsv
[2023-03-19 04:11:40,659] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:11:40,659] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:11:40,659] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg965c00a2-60b6-41c5-99d0-c0c4e52c37dd/dqc_reference/checkm_data
[2023-03-19 04:11:40,660] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:11:40,664] [INFO] Task started: CheckM
[2023-03-19 04:11:40,664] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7470/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7470/checkm_input OceanDNA-b7470/checkm_result
[2023-03-19 04:12:25,778] [INFO] Task succeeded: CheckM
[2023-03-19 04:12:25,778] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:12:25,780] [INFO] ===== Completeness check finished =====
[2023-03-19 04:12:25,780] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:12:25,780] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7470/markers.fasta)
[2023-03-19 04:12:25,781] [INFO] Task started: Blastn
[2023-03-19 04:12:25,781] [INFO] Running command: blastn -query OceanDNA-b7470/markers.fasta -db /var/lib/cwl/stg965c00a2-60b6-41c5-99d0-c0c4e52c37dd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7470/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:12:26,718] [INFO] Task succeeded: Blastn
[2023-03-19 04:12:26,719] [INFO] Selected 9 target genomes.
[2023-03-19 04:12:26,719] [INFO] Target genome list was writen to OceanDNA-b7470/target_genomes_gtdb.txt
[2023-03-19 04:12:26,784] [INFO] Task started: fastANI
[2023-03-19 04:12:26,784] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9ce63ca-84bc-4c0a-a3e7-5c15be836c3c/OceanDNA-b7470.fa --refList OceanDNA-b7470/target_genomes_gtdb.txt --output OceanDNA-b7470/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:12:33,456] [INFO] Task succeeded: fastANI
[2023-03-19 04:12:33,462] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 04:12:33,462] [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_001874145.1	s__Lacinutrix sp001874145	99.9746	992	1011	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000211855.2	s__Lacinutrix sp000211855	94.2783	913	1011	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003663945.1	s__Lacinutrix venerupis	83.0265	690	1011	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	98.08	98.08	0.92	0.92	2	-
GCF_001418085.1	s__Lacinutrix algicola	80.6844	603	1011	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002831665.1	s__Lacinutrix sp002831665	80.3888	621	1011	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418015.1	s__Lacinutrix mariniflava	80.1256	634	1011	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000797445.1	s__Lacinutrix jangbogonensis	79.7305	522	1011	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016864015.1	s__Oceanihabitans sp016864015	78.7946	445	1011	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014764305.1	s__Mesoflavibacter profundi	78.6671	470	1011	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesoflavibacter	95.0	99.53	99.53	0.98	0.98	3	-
--------------------------------------------------------------------------------
[2023-03-19 04:12:33,462] [INFO] GTDB search result was written to OceanDNA-b7470/result_gtdb.tsv
[2023-03-19 04:12:33,462] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:12:33,464] [INFO] DFAST_QC result json was written to OceanDNA-b7470/dqc_result.json
[2023-03-19 04:12:33,464] [INFO] DFAST_QC completed!
[2023-03-19 04:12:33,464] [INFO] Total running time: 0h1m27s