[2023-03-18 23:27:53,696] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:27:53,696] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:27:53,696] [INFO] DQC Reference Directory: /var/lib/cwl/stg70853dd4-0f37-464c-9c31-588d0edbee6b/dqc_reference
[2023-03-18 23:27:55,547] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:27:55,547] [INFO] Task started: Prodigal
[2023-03-18 23:27:55,548] [INFO] Running command: cat /var/lib/cwl/stg4584fc87-d820-46ad-af2e-193a35ce02b2/OceanDNA-b9635.fa | prodigal -d OceanDNA-b9635/cds.fna -a OceanDNA-b9635/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:28:09,173] [INFO] Task succeeded: Prodigal
[2023-03-18 23:28:09,173] [INFO] Task started: HMMsearch
[2023-03-18 23:28:09,173] [INFO] Running command: hmmsearch --tblout OceanDNA-b9635/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg70853dd4-0f37-464c-9c31-588d0edbee6b/dqc_reference/reference_markers.hmm OceanDNA-b9635/protein.faa > /dev/null
[2023-03-18 23:28:09,360] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:28:09,361] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4584fc87-d820-46ad-af2e-193a35ce02b2/OceanDNA-b9635.fa]
[2023-03-18 23:28:09,376] [INFO] Query marker FASTA was written to OceanDNA-b9635/markers.fasta
[2023-03-18 23:28:09,378] [INFO] Task started: Blastn
[2023-03-18 23:28:09,378] [INFO] Running command: blastn -query OceanDNA-b9635/markers.fasta -db /var/lib/cwl/stg70853dd4-0f37-464c-9c31-588d0edbee6b/dqc_reference/reference_markers.fasta -out OceanDNA-b9635/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:28:10,004] [INFO] Task succeeded: Blastn
[2023-03-18 23:28:10,005] [INFO] Selected 23 target genomes.
[2023-03-18 23:28:10,005] [INFO] Target genome list was writen to OceanDNA-b9635/target_genomes.txt
[2023-03-18 23:28:10,020] [INFO] Task started: fastANI
[2023-03-18 23:28:10,020] [INFO] Running command: fastANI --query /var/lib/cwl/stg4584fc87-d820-46ad-af2e-193a35ce02b2/OceanDNA-b9635.fa --refList OceanDNA-b9635/target_genomes.txt --output OceanDNA-b9635/fastani_result.tsv --threads 1
[2023-03-18 23:28:24,303] [INFO] Task succeeded: fastANI
[2023-03-18 23:28:24,303] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg70853dd4-0f37-464c-9c31-588d0edbee6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:28:24,304] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg70853dd4-0f37-464c-9c31-588d0edbee6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:28:24,314] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:28:24,314] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 23:28:24,314] [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
Maribacter ulvicola	strain=DSM 15366	GCA_900155985.1	228959	228959	type	True	77.4558	142	716	95	below_threshold
Maribacter spongiicola	strain=DSM 25233	GCA_004364165.1	1206753	1206753	type	True	76.934	148	716	95	below_threshold
Maribacter arcticus	strain=DSM 23546	GCA_900167935.1	561365	561365	type	True	76.8747	139	716	95	below_threshold
Maribacter aquivivus	strain=DSM 16478	GCA_900142175.1	228958	228958	type	True	76.8638	163	716	95	below_threshold
Maribacter dokdonensis	strain=DSW-8	GCA_001447995.1	320912	320912	type	True	76.7845	125	716	95	below_threshold
Maribacter caenipelagi	strain=CECT 8455	GCA_004364175.1	1447781	1447781	type	True	76.763	167	716	95	below_threshold
Maribacter orientalis	strain=DSM 16471	GCA_900109345.1	228957	228957	type	True	76.7337	140	716	95	below_threshold
Cellulophaga omnivescoria	strain=W5C	GCA_001999725.1	1888890	1888890	type	True	76.7068	133	716	95	below_threshold
Maribacter hydrothermalis	strain=T28	GCA_001913155.1	1836467	1836467	type	True	76.652	144	716	95	below_threshold
Cellulophaga tyrosinoxydans	strain=DSM 21164	GCA_900176415.1	504486	504486	type	True	76.4968	124	716	95	below_threshold
Zobellia barbeyronii	strain=KMM 6746	GCA_018603515.1	2748009	2748009	type	True	76.4041	111	716	95	below_threshold
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	76.1386	69	716	95	below_threshold
Winogradskyella eckloniae	strain=EC29	GCA_013249045.1	1089306	1089306	type	True	75.7024	59	716	95	below_threshold
Croceivirga lutea	strain=CGMCC 1.15761	GCA_014643615.1	1775167	1775167	type	True	75.6897	80	716	95	below_threshold
Croceivirga lutea	strain=CSW06	GCA_014235875.1	1775167	1775167	type	True	75.6585	82	716	95	below_threshold
Aquimarina muelleri	strain=KCTC 12285	GCA_014651355.1	279356	279356	type	True	75.6017	57	716	95	below_threshold
Aquimarina muelleri	strain=DSM 19832	GCA_000430665.1	279356	279356	type	True	75.6017	57	716	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 23:28:24,314] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9635/tc_result.tsv
[2023-03-18 23:28:24,314] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:28:24,315] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:28:24,315] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg70853dd4-0f37-464c-9c31-588d0edbee6b/dqc_reference/checkm_data
[2023-03-18 23:28:24,315] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:28:24,319] [INFO] Task started: CheckM
[2023-03-18 23:28:24,319] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9635/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9635/checkm_input OceanDNA-b9635/checkm_result
[2023-03-18 23:29:01,224] [INFO] Task succeeded: CheckM
[2023-03-18 23:29:01,225] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:29:01,227] [INFO] ===== Completeness check finished =====
[2023-03-18 23:29:01,227] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:29:01,227] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9635/markers.fasta)
[2023-03-18 23:29:01,228] [INFO] Task started: Blastn
[2023-03-18 23:29:01,229] [INFO] Running command: blastn -query OceanDNA-b9635/markers.fasta -db /var/lib/cwl/stg70853dd4-0f37-464c-9c31-588d0edbee6b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9635/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:29:02,140] [INFO] Task succeeded: Blastn
[2023-03-18 23:29:02,141] [INFO] Selected 25 target genomes.
[2023-03-18 23:29:02,142] [INFO] Target genome list was writen to OceanDNA-b9635/target_genomes_gtdb.txt
[2023-03-18 23:29:02,167] [INFO] Task started: fastANI
[2023-03-18 23:29:02,167] [INFO] Running command: fastANI --query /var/lib/cwl/stg4584fc87-d820-46ad-af2e-193a35ce02b2/OceanDNA-b9635.fa --refList OceanDNA-b9635/target_genomes_gtdb.txt --output OceanDNA-b9635/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:29:17,429] [INFO] Task succeeded: fastANI
[2023-03-18 23:29:17,440] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 23:29:17,441] [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_900155985.1	s__Maribacter ulvicola	77.4364	143	716	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112245.1	s__Maribacter stanieri	77.0808	157	716	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	98.09	98.09	0.92	0.92	2	-
GCA_011050675.1	s__Maribacter sp011050675	77.004	153	716	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	100.00	100.00	0.99	0.99	2	-
GCF_004364165.1	s__Maribacter spongiicola	76.934	148	716	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167935.1	s__Maribacter arcticus	76.8747	139	716	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142175.1	s__Maribacter aquivivus	76.8618	163	716	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001447995.1	s__Maribacter dokdonensis	76.7845	125	716	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	97.64	97.51	0.89	0.86	13	-
GCF_004364175.1	s__Maribacter caenipelagi	76.763	167	716	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634105.1	s__Maribacter_B vaceletii	76.7392	169	716	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109345.1	s__Maribacter orientalis	76.7337	140	716	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001999725.1	s__Cellulophaga omnivescoria	76.7209	132	716	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001913155.1	s__Maribacter hydrothermalis	76.652	144	716	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900119145.1	s__Cellulophaga fucicola	76.633	132	716	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019021925.1	s__Cellulophaga sp019021925	76.5279	126	716	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176415.1	s__Cellulophaga tyrosinoxydans	76.4778	124	716	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418105.1	s__Oceanihabitans himadriensis	76.1625	68	716	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008084905.1	s__Xanthomarina maritima	75.8099	53	716	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013249045.1	s__Winogradskyella eckloniae	75.7024	59	716	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014235875.1	s__Croceivirga lutea	75.6439	81	716	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Croceivirga	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-18 23:29:17,441] [INFO] GTDB search result was written to OceanDNA-b9635/result_gtdb.tsv
[2023-03-18 23:29:17,441] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:29:17,443] [INFO] DFAST_QC result json was written to OceanDNA-b9635/dqc_result.json
[2023-03-18 23:29:17,443] [INFO] DFAST_QC completed!
[2023-03-18 23:29:17,443] [INFO] Total running time: 0h1m24s