[2023-03-15 22:44:22,348] [INFO] DFAST_QC pipeline started.
[2023-03-15 22:44:22,348] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 22:44:22,348] [INFO] DQC Reference Directory: /var/lib/cwl/stga0266280-d792-4cfa-8256-0f4dccce1987/dqc_reference
[2023-03-15 22:44:23,461] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 22:44:23,461] [INFO] Task started: Prodigal
[2023-03-15 22:44:23,461] [INFO] Running command: cat /var/lib/cwl/stgec603557-26e3-431f-a032-de4fafb1f47d/OceanDNA-b7206.fa | prodigal -d OceanDNA-b7206/cds.fna -a OceanDNA-b7206/protein.faa -g 11 -q > /dev/null
[2023-03-15 22:44:42,619] [INFO] Task succeeded: Prodigal
[2023-03-15 22:44:42,619] [INFO] Task started: HMMsearch
[2023-03-15 22:44:42,619] [INFO] Running command: hmmsearch --tblout OceanDNA-b7206/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga0266280-d792-4cfa-8256-0f4dccce1987/dqc_reference/reference_markers.hmm OceanDNA-b7206/protein.faa > /dev/null
[2023-03-15 22:44:42,844] [INFO] Task succeeded: HMMsearch
[2023-03-15 22:44:42,845] [INFO] Found 6/6 markers.
[2023-03-15 22:44:42,897] [INFO] Query marker FASTA was written to OceanDNA-b7206/markers.fasta
[2023-03-15 22:44:42,897] [INFO] Task started: Blastn
[2023-03-15 22:44:42,897] [INFO] Running command: blastn -query OceanDNA-b7206/markers.fasta -db /var/lib/cwl/stga0266280-d792-4cfa-8256-0f4dccce1987/dqc_reference/reference_markers.fasta -out OceanDNA-b7206/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:44:43,470] [INFO] Task succeeded: Blastn
[2023-03-15 22:44:43,477] [INFO] Selected 12 target genomes.
[2023-03-15 22:44:43,478] [INFO] Target genome list was writen to OceanDNA-b7206/target_genomes.txt
[2023-03-15 22:44:43,484] [INFO] Task started: fastANI
[2023-03-15 22:44:43,484] [INFO] Running command: fastANI --query /var/lib/cwl/stgec603557-26e3-431f-a032-de4fafb1f47d/OceanDNA-b7206.fa --refList OceanDNA-b7206/target_genomes.txt --output OceanDNA-b7206/fastani_result.tsv --threads 1
[2023-03-15 22:44:51,125] [INFO] Task succeeded: fastANI
[2023-03-15 22:44:51,125] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga0266280-d792-4cfa-8256-0f4dccce1987/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 22:44:51,125] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga0266280-d792-4cfa-8256-0f4dccce1987/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 22:44:51,132] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 22:44:51,132] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 22:44:51,132] [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
Gramella forsetii	strain=KT0803	GCA_000060345.1	411153	411153	type	True	81.7638	694	973	95	below_threshold
Gramella forsetii	strain=CGMCC 1.15422	GCA_014642775.1	411153	411153	type	True	81.7074	690	973	95	below_threshold
Gramella gaetbulicola	strain=DSM 23082	GCA_003054225.1	703340	703340	type	True	79.9973	507	973	95	below_threshold
Gramella echinicola	strain=DSM 19838	GCA_000423065.1	279359	279359	type	True	79.8468	504	973	95	below_threshold
Gramella lutea	strain=YJ019	GCA_022489035.1	1607951	1607951	type	True	79.3389	464	973	95	below_threshold
Gramella salexigens	strain=LPB0144	GCA_001889005.1	1913577	1913577	type	True	78.7932	344	973	95	below_threshold
Gramella portivictoriae	strain=DSM 23547	GCA_000423045.1	326069	326069	type	True	78.509	334	973	95	below_threshold
Gramella crocea	strain=YB25	GCA_022410465.1	2904124	2904124	type	True	78.4827	381	973	95	below_threshold
Salegentibacter salarius	strain=KCTC 12974	GCA_002833385.1	435906	435906	type	True	77.2902	231	973	95	below_threshold
Salegentibacter lacus	strain=LM13S	GCA_020164555.1	2873599	2873599	type	True	76.8463	238	973	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 22:44:51,137] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7206/tc_result.tsv
[2023-03-15 22:44:51,139] [INFO] ===== Taxonomy check completed =====
[2023-03-15 22:44:51,139] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 22:44:51,139] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga0266280-d792-4cfa-8256-0f4dccce1987/dqc_reference/checkm_data
[2023-03-15 22:44:51,140] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 22:44:51,226] [INFO] Task started: CheckM
[2023-03-15 22:44:51,226] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7206/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7206/checkm_input OceanDNA-b7206/checkm_result
[2023-03-15 22:45:41,570] [INFO] Task succeeded: CheckM
[2023-03-15 22:45:41,570] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.74%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 22:45:41,630] [INFO] ===== Completeness check finished =====
[2023-03-15 22:45:41,630] [INFO] ===== Start GTDB Search =====
[2023-03-15 22:45:41,630] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7206/markers.fasta)
[2023-03-15 22:45:41,631] [INFO] Task started: Blastn
[2023-03-15 22:45:41,631] [INFO] Running command: blastn -query OceanDNA-b7206/markers.fasta -db /var/lib/cwl/stga0266280-d792-4cfa-8256-0f4dccce1987/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7206/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:45:42,443] [INFO] Task succeeded: Blastn
[2023-03-15 22:45:42,451] [INFO] Selected 9 target genomes.
[2023-03-15 22:45:42,452] [INFO] Target genome list was writen to OceanDNA-b7206/target_genomes_gtdb.txt
[2023-03-15 22:45:42,510] [INFO] Task started: fastANI
[2023-03-15 22:45:42,510] [INFO] Running command: fastANI --query /var/lib/cwl/stgec603557-26e3-431f-a032-de4fafb1f47d/OceanDNA-b7206.fa --refList OceanDNA-b7206/target_genomes_gtdb.txt --output OceanDNA-b7206/fastani_result_gtdb.tsv --threads 1
[2023-03-15 22:45:48,596] [INFO] Task succeeded: fastANI
[2023-03-15 22:45:48,602] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 22:45:48,602] [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_000060345.1	s__Gramella forsetii	81.7465	696	973	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900105135.1	s__Gramella sp900105135	81.5992	639	973	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054225.1	s__Gramella gaetbulicola	79.9974	506	973	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423065.1	s__Gramella echinicola	79.8592	502	973	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	97.44	97.44	0.87	0.87	2	-
GCF_007050985.1	s__Gramella sabulilitoris	79.3617	448	973	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001889005.1	s__Gramella salexigens	78.7806	345	973	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006714895.1	s__Gramella sp006714895	78.6347	378	973	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423045.1	s__Gramella portivictoriae	78.509	334	973	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900168265.1	s__Salegentibacter salarius	77.2626	236	973	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	100.00	99.99	1.00	0.99	3	-
--------------------------------------------------------------------------------
[2023-03-15 22:45:48,605] [INFO] GTDB search result was written to OceanDNA-b7206/result_gtdb.tsv
[2023-03-15 22:45:48,612] [INFO] ===== GTDB Search completed =====
[2023-03-15 22:45:48,618] [INFO] DFAST_QC result json was written to OceanDNA-b7206/dqc_result.json
[2023-03-15 22:45:48,618] [INFO] DFAST_QC completed!
[2023-03-15 22:45:48,618] [INFO] Total running time: 0h1m26s