[2023-03-15 13:45:07,866] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:45:07,866] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:45:07,866] [INFO] DQC Reference Directory: /var/lib/cwl/stgfdf99e23-9626-404f-bd31-be1114538d97/dqc_reference
[2023-03-15 13:45:09,269] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:45:09,270] [INFO] Task started: Prodigal
[2023-03-15 13:45:09,270] [INFO] Running command: cat /var/lib/cwl/stg858ec584-b933-4c9d-81dd-9fc98b9236ec/OceanDNA-b7187.fa | prodigal -d OceanDNA-b7187/cds.fna -a OceanDNA-b7187/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:45:30,511] [INFO] Task succeeded: Prodigal
[2023-03-15 13:45:30,511] [INFO] Task started: HMMsearch
[2023-03-15 13:45:30,511] [INFO] Running command: hmmsearch --tblout OceanDNA-b7187/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfdf99e23-9626-404f-bd31-be1114538d97/dqc_reference/reference_markers.hmm OceanDNA-b7187/protein.faa > /dev/null
[2023-03-15 13:45:30,731] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:45:30,731] [INFO] Found 6/6 markers.
[2023-03-15 13:45:30,754] [INFO] Query marker FASTA was written to OceanDNA-b7187/markers.fasta
[2023-03-15 13:45:30,754] [INFO] Task started: Blastn
[2023-03-15 13:45:30,754] [INFO] Running command: blastn -query OceanDNA-b7187/markers.fasta -db /var/lib/cwl/stgfdf99e23-9626-404f-bd31-be1114538d97/dqc_reference/reference_markers.fasta -out OceanDNA-b7187/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:45:31,369] [INFO] Task succeeded: Blastn
[2023-03-15 13:45:31,370] [INFO] Selected 22 target genomes.
[2023-03-15 13:45:31,371] [INFO] Target genome list was writen to OceanDNA-b7187/target_genomes.txt
[2023-03-15 13:45:31,386] [INFO] Task started: fastANI
[2023-03-15 13:45:31,386] [INFO] Running command: fastANI --query /var/lib/cwl/stg858ec584-b933-4c9d-81dd-9fc98b9236ec/OceanDNA-b7187.fa --refList OceanDNA-b7187/target_genomes.txt --output OceanDNA-b7187/fastani_result.tsv --threads 1
[2023-03-15 13:45:44,909] [INFO] Task succeeded: fastANI
[2023-03-15 13:45:44,910] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfdf99e23-9626-404f-bd31-be1114538d97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:45:44,910] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfdf99e23-9626-404f-bd31-be1114538d97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:45:44,922] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:45:44,922] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 13:45:44,923] [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
Gillisia hiemivivida	strain=IC154	GCA_007997295.1	291190	291190	type	True	79.0255	409	1117	95	below_threshold
Gillisia mitskevichiae	strain=DSM 19839	GCA_003634585.1	270921	270921	type	True	78.6639	391	1117	95	below_threshold
Gillisia marina	strain=CBA3202	GCA_000258765.1	1167637	1167637	type	True	78.0115	323	1117	95	below_threshold
Gillisia limnaea	strain=DSM 15749	GCA_000243235.1	195907	195907	type	True	77.8672	298	1117	95	below_threshold
Antarcticibacterium flavum	strain=KCTC 52984	GCA_006159205.1	2058175	2058175	type	True	77.3956	198	1117	95	below_threshold
Antarcticibacterium arcticum	strain=PAMC 28998	GCA_007993795.1	2585771	2585771	type	True	77.2986	209	1117	95	below_threshold
Salegentibacter salarius	strain=KCTC 12974	GCA_002833385.1	435906	435906	type	True	77.0002	193	1117	95	below_threshold
Salegentibacter salarius	strain=DSM 23401	GCA_900168265.1	435906	435906	type	True	76.9857	193	1117	95	below_threshold
Salegentibacter salegens	strain=ACAM 48	GCA_900142975.1	143223	143223	type	True	76.9485	205	1117	95	below_threshold
Salegentibacter agarivorans	strain=DSM 23515	GCA_900113135.1	345907	345907	type	True	76.9434	214	1117	95	below_threshold
Salegentibacter salegens	strain=DSM 5424	GCA_003001895.1	143223	143223	type	True	76.924	199	1117	95	below_threshold
Salegentibacter holothuriorum	strain=DSM 23405	GCA_900168045.1	241145	241145	type	True	76.8517	196	1117	95	below_threshold
Gramella crocea	strain=YB25	GCA_022410465.1	2904124	2904124	type	True	76.5124	122	1117	95	below_threshold
Salinimicrobium catena	strain=CGMCC 1.6101	GCA_900102915.1	390640	390640	type	True	76.3585	84	1117	95	below_threshold
Salinimicrobium catena	strain=DSM 23553	GCA_900107495.1	390640	390640	type	True	76.3196	83	1117	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	76.0609	64	1117	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	75.9228	80	1117	95	below_threshold
Aquimarina amphilecti	strain=DSM 25232	GCA_900109375.1	1038014	1038014	type	True	75.9194	102	1117	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	75.8702	71	1117	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	75.5734	89	1117	95	below_threshold
Flavobacterium profundi	strain=TP390	GCA_009753805.1	1774945	1774945	type	True	75.5319	78	1117	95	below_threshold
Halomarinibacterium sedimenti	strain=CAU 1614	GCA_019312585.1	2857106	2857106	type	True	75.5079	64	1117	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 13:45:44,923] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7187/tc_result.tsv
[2023-03-15 13:45:44,923] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:45:44,923] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:45:44,923] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfdf99e23-9626-404f-bd31-be1114538d97/dqc_reference/checkm_data
[2023-03-15 13:45:44,924] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:45:44,943] [INFO] Task started: CheckM
[2023-03-15 13:45:44,943] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7187/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7187/checkm_input OceanDNA-b7187/checkm_result
[2023-03-15 13:46:38,535] [INFO] Task succeeded: CheckM
[2023-03-15 13:46:38,535] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.43%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 13:46:38,539] [INFO] ===== Completeness check finished =====
[2023-03-15 13:46:38,540] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:46:38,540] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7187/markers.fasta)
[2023-03-15 13:46:38,541] [INFO] Task started: Blastn
[2023-03-15 13:46:38,541] [INFO] Running command: blastn -query OceanDNA-b7187/markers.fasta -db /var/lib/cwl/stgfdf99e23-9626-404f-bd31-be1114538d97/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7187/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:46:39,401] [INFO] Task succeeded: Blastn
[2023-03-15 13:46:39,403] [INFO] Selected 14 target genomes.
[2023-03-15 13:46:39,403] [INFO] Target genome list was writen to OceanDNA-b7187/target_genomes_gtdb.txt
[2023-03-15 13:46:39,419] [INFO] Task started: fastANI
[2023-03-15 13:46:39,419] [INFO] Running command: fastANI --query /var/lib/cwl/stg858ec584-b933-4c9d-81dd-9fc98b9236ec/OceanDNA-b7187.fa --refList OceanDNA-b7187/target_genomes_gtdb.txt --output OceanDNA-b7187/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:46:49,063] [INFO] Task succeeded: fastANI
[2023-03-15 13:46:49,071] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 13:46:49,072] [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_900104765.1	s__Gillisia sp900104765	83.9729	747	1117	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	98.23	98.23	0.92	0.92	2	-
GCF_000403785.1	s__Gillisia sp000403785	79.0333	418	1117	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997295.1	s__Gillisia hiemivivida	79.0311	408	1117	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	95.35	95.35	0.83	0.83	2	-
GCA_002364325.1	s__Gillisia sp002364325	78.7366	291	1117	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634585.1	s__Gillisia mitskevichiae	78.6561	393	1117	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000258765.1	s__Gillisia marina	78.0	324	1117	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000243235.1	s__Gillisia limnaea	77.8708	295	1117	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007827275.1	s__Gillisia sp007827275	77.8551	297	1117	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142975.1	s__Salegentibacter salegens	76.9486	204	1117	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900113135.1	s__Salegentibacter agarivorans	76.941	216	1117	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	97.64	95.65	0.87	0.86	4	-
GCF_900168045.1	s__Salegentibacter holothuriorum	76.8519	196	1117	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102915.1	s__Salinimicrobium catena	76.3585	84	1117	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salinimicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002414705.1	s__Algorimicrobium sp002414705	75.963	67	1117	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222875.1	s__Psychroserpens sp018222875	75.9374	60	1117	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 13:46:49,072] [INFO] GTDB search result was written to OceanDNA-b7187/result_gtdb.tsv
[2023-03-15 13:46:49,073] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:46:49,076] [INFO] DFAST_QC result json was written to OceanDNA-b7187/dqc_result.json
[2023-03-15 13:46:49,076] [INFO] DFAST_QC completed!
[2023-03-15 13:46:49,076] [INFO] Total running time: 0h1m41s