[2023-03-15 21:48:06,724] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:48:06,724] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:48:06,724] [INFO] DQC Reference Directory: /var/lib/cwl/stg2e145370-8371-4add-9277-399343c6ac50/dqc_reference
[2023-03-15 21:48:07,835] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:48:07,836] [INFO] Task started: Prodigal
[2023-03-15 21:48:07,836] [INFO] Running command: cat /var/lib/cwl/stg6bcecb85-0aa5-4812-8b2d-8017b3e351f6/OceanDNA-b7191.fa | prodigal -d OceanDNA-b7191/cds.fna -a OceanDNA-b7191/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:48:24,992] [INFO] Task succeeded: Prodigal
[2023-03-15 21:48:24,992] [INFO] Task started: HMMsearch
[2023-03-15 21:48:24,992] [INFO] Running command: hmmsearch --tblout OceanDNA-b7191/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2e145370-8371-4add-9277-399343c6ac50/dqc_reference/reference_markers.hmm OceanDNA-b7191/protein.faa > /dev/null
[2023-03-15 21:48:25,194] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:48:25,194] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6bcecb85-0aa5-4812-8b2d-8017b3e351f6/OceanDNA-b7191.fa]
[2023-03-15 21:48:25,211] [INFO] Query marker FASTA was written to OceanDNA-b7191/markers.fasta
[2023-03-15 21:48:25,212] [INFO] Task started: Blastn
[2023-03-15 21:48:25,212] [INFO] Running command: blastn -query OceanDNA-b7191/markers.fasta -db /var/lib/cwl/stg2e145370-8371-4add-9277-399343c6ac50/dqc_reference/reference_markers.fasta -out OceanDNA-b7191/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:48:25,832] [INFO] Task succeeded: Blastn
[2023-03-15 21:48:25,833] [INFO] Selected 15 target genomes.
[2023-03-15 21:48:25,833] [INFO] Target genome list was writen to OceanDNA-b7191/target_genomes.txt
[2023-03-15 21:48:25,849] [INFO] Task started: fastANI
[2023-03-15 21:48:25,849] [INFO] Running command: fastANI --query /var/lib/cwl/stg6bcecb85-0aa5-4812-8b2d-8017b3e351f6/OceanDNA-b7191.fa --refList OceanDNA-b7191/target_genomes.txt --output OceanDNA-b7191/fastani_result.tsv --threads 1
[2023-03-15 21:48:34,389] [INFO] Task succeeded: fastANI
[2023-03-15 21:48:34,389] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2e145370-8371-4add-9277-399343c6ac50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:48:34,390] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2e145370-8371-4add-9277-399343c6ac50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:48:34,399] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:48:34,399] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 21:48:34,399] [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	82.0884	587	890	95	below_threshold
Gillisia mitskevichiae	strain=DSM 19839	GCA_003634585.1	270921	270921	type	True	81.254	543	890	95	below_threshold
Gillisia marina	strain=CBA3202	GCA_000258765.1	1167637	1167637	type	True	80.5955	511	890	95	below_threshold
Antarcticibacterium flavum	strain=KCTC 52984	GCA_006159205.1	2058175	2058175	type	True	77.9279	154	890	95	below_threshold
Antarcticibacterium arcticum	strain=PAMC 28998	GCA_007993795.1	2585771	2585771	type	True	77.9069	182	890	95	below_threshold
Gillisia limnaea	strain=DSM 15749	GCA_000243235.1	195907	195907	type	True	77.7674	246	890	95	below_threshold
Gramella salexigens	strain=LPB0144	GCA_001889005.1	1913577	1913577	type	True	77.0058	131	890	95	below_threshold
Oceanihabitans sediminis	strain=S9-10	GCA_003337215.1	1812012	1812012	type	True	76.8277	77	890	95	below_threshold
Oceanihabitans sediminis	strain=DSM 28133	GCA_003315315.1	1812012	1812012	type	True	76.8188	77	890	95	below_threshold
Mesonia phycicola	strain=DSM 21425	GCA_900141885.1	579105	579105	type	True	76.8135	122	890	95	below_threshold
Zunongwangia atlantica	strain=22II14-10F7	GCA_002094855.1	1502297	1502297	type	True	76.7513	149	890	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	76.6474	56	890	95	below_threshold
Salegentibacter echinorum	strain=DSM 24579	GCA_900129445.1	1073325	1073325	type	True	76.6205	122	890	95	below_threshold
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	76.5522	78	890	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 21:48:34,399] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7191/tc_result.tsv
[2023-03-15 21:48:34,399] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:48:34,399] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:48:34,400] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2e145370-8371-4add-9277-399343c6ac50/dqc_reference/checkm_data
[2023-03-15 21:48:34,400] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:48:34,407] [INFO] Task started: CheckM
[2023-03-15 21:48:34,407] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7191/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7191/checkm_input OceanDNA-b7191/checkm_result
[2023-03-15 21:49:18,862] [INFO] Task succeeded: CheckM
[2023-03-15 21:49:18,863] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 21:49:18,867] [INFO] ===== Completeness check finished =====
[2023-03-15 21:49:18,867] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:49:18,867] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7191/markers.fasta)
[2023-03-15 21:49:18,867] [INFO] Task started: Blastn
[2023-03-15 21:49:18,867] [INFO] Running command: blastn -query OceanDNA-b7191/markers.fasta -db /var/lib/cwl/stg2e145370-8371-4add-9277-399343c6ac50/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7191/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:49:19,837] [INFO] Task succeeded: Blastn
[2023-03-15 21:49:19,839] [INFO] Selected 10 target genomes.
[2023-03-15 21:49:19,839] [INFO] Target genome list was writen to OceanDNA-b7191/target_genomes_gtdb.txt
[2023-03-15 21:49:19,924] [INFO] Task started: fastANI
[2023-03-15 21:49:19,924] [INFO] Running command: fastANI --query /var/lib/cwl/stg6bcecb85-0aa5-4812-8b2d-8017b3e351f6/OceanDNA-b7191.fa --refList OceanDNA-b7191/target_genomes_gtdb.txt --output OceanDNA-b7191/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:49:26,574] [INFO] Task succeeded: fastANI
[2023-03-15 21:49:26,581] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 21:49:26,581] [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_002364325.1	s__Gillisia sp002364325	99.956	681	890	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007997295.1	s__Gillisia hiemivivida	82.1015	586	890	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	95.35	95.35	0.83	0.83	2	-
GCF_000403785.1	s__Gillisia sp000403785	81.5975	574	890	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	81.2515	542	890	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	80.5899	512	890	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	80.2768	513	890	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001889005.1	s__Gramella salexigens	77.0058	131	890	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002094855.1	s__Zunongwangia atlantica	76.7518	150	890	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zunongwangia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860825.1	s__Oceanihabitans sp018860825	76.3647	80	890	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016864015.1	s__Oceanihabitans sp016864015	76.3405	97	890	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 21:49:26,583] [INFO] GTDB search result was written to OceanDNA-b7191/result_gtdb.tsv
[2023-03-15 21:49:26,583] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:49:26,585] [INFO] DFAST_QC result json was written to OceanDNA-b7191/dqc_result.json
[2023-03-15 21:49:26,585] [INFO] DFAST_QC completed!
[2023-03-15 21:49:26,585] [INFO] Total running time: 0h1m20s