[2023-03-17 23:06:29,019] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:06:29,019] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:06:29,019] [INFO] DQC Reference Directory: /var/lib/cwl/stgdfdef96c-4f5f-4be8-9523-d93d624cee35/dqc_reference
[2023-03-17 23:06:30,154] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:06:30,155] [INFO] Task started: Prodigal
[2023-03-17 23:06:30,155] [INFO] Running command: cat /var/lib/cwl/stg1afcda53-1816-4e44-b84e-ab8626c872e7/OceanDNA-b6750.fa | prodigal -d OceanDNA-b6750/cds.fna -a OceanDNA-b6750/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:06:48,553] [INFO] Task succeeded: Prodigal
[2023-03-17 23:06:48,553] [INFO] Task started: HMMsearch
[2023-03-17 23:06:48,553] [INFO] Running command: hmmsearch --tblout OceanDNA-b6750/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdfdef96c-4f5f-4be8-9523-d93d624cee35/dqc_reference/reference_markers.hmm OceanDNA-b6750/protein.faa > /dev/null
[2023-03-17 23:06:48,742] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:06:48,743] [INFO] Found 6/6 markers.
[2023-03-17 23:06:48,772] [INFO] Query marker FASTA was written to OceanDNA-b6750/markers.fasta
[2023-03-17 23:06:48,775] [INFO] Task started: Blastn
[2023-03-17 23:06:48,775] [INFO] Running command: blastn -query OceanDNA-b6750/markers.fasta -db /var/lib/cwl/stgdfdef96c-4f5f-4be8-9523-d93d624cee35/dqc_reference/reference_markers.fasta -out OceanDNA-b6750/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:06:49,334] [INFO] Task succeeded: Blastn
[2023-03-17 23:06:49,336] [INFO] Selected 26 target genomes.
[2023-03-17 23:06:49,336] [INFO] Target genome list was writen to OceanDNA-b6750/target_genomes.txt
[2023-03-17 23:06:49,349] [INFO] Task started: fastANI
[2023-03-17 23:06:49,350] [INFO] Running command: fastANI --query /var/lib/cwl/stg1afcda53-1816-4e44-b84e-ab8626c872e7/OceanDNA-b6750.fa --refList OceanDNA-b6750/target_genomes.txt --output OceanDNA-b6750/fastani_result.tsv --threads 1
[2023-03-17 23:07:05,496] [INFO] Task succeeded: fastANI
[2023-03-17 23:07:05,497] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdfdef96c-4f5f-4be8-9523-d93d624cee35/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:07:05,497] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdfdef96c-4f5f-4be8-9523-d93d624cee35/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:07:05,510] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:07:05,510] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 23:07:05,510] [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
Muricauda algicola	strain=AsT0115	GCA_005937185.1	2583815	2583815	type	True	78.7869	317	684	95	below_threshold
Muricauda flava	strain=DSM 22638	GCA_900129665.1	570519	570519	type	True	78.343	270	684	95	below_threshold
Muricauda parva	strain=DSM 25885	GCA_900215465.1	1247520	1247520	type	True	78.0167	212	684	95	below_threshold
Muricauda onchidii	strain=XY-359	GCA_004804315.1	2562684	2562684	type	True	77.983	213	684	95	below_threshold
Muricauda nanhaiensis	strain=SM1704	GCA_003382275.1	2292706	2292706	type	True	77.8563	182	684	95	below_threshold
Muricauda chongwuensis	strain=HICW	GCA_013376415.1	2697365	2697365	type	True	77.6637	129	684	95	below_threshold
Muricauda olearia	strain=CL-SS4	GCA_009184425.1	552546	552546	type	True	77.6207	176	684	95	below_threshold
Muricauda aequoris	strain=NH166	GCA_008017345.1	2306997	2306997	type	True	77.6043	133	684	95	below_threshold
Muricauda aquimarina	strain=JCM11811	GCA_003992675.1	254955	254955	type	True	77.5833	132	684	95	below_threshold
Muricauda brasiliensis	strain=K001	GCA_003057865.1	2162892	2162892	type	True	77.5274	130	684	95	below_threshold
Muricauda aurea	strain=BC31-1-A7	GCA_017313785.1	2915619	2915619	type	True	77.4842	133	684	95	below_threshold
Muricauda maritima	strain=72	GCA_003584135.1	2306998	2306998	type	True	77.4756	137	684	95	below_threshold
Muricauda maritima	strain=72	GCA_008017365.1	2306998	2306998	type	True	77.4756	137	684	95	below_threshold
Muricauda oceani	strain=501str8	GCA_019457985.1	2698672	2698672	type	True	77.4399	139	684	95	below_threshold
Muricauda oceani	strain=501str8	GCA_011068285.1	2698672	2698672	type	True	77.4169	139	684	95	below_threshold
Muricauda amphidinii	strain=LMIT004	GCA_013090115.1	2735167	2735167	type	True	77.3328	218	684	95	below_threshold
Costertonia aggregata	strain=KCCM 42265	GCA_013402795.1	343403	343403	type	True	76.5776	65	684	95	below_threshold
Maribacter polysiphoniae	strain=KCTC 22021	GCA_014673435.1	429344	429344	type	True	76.3844	62	684	95	below_threshold
Maribacter polysiphoniae	strain=DSM 23514	GCA_003148665.1	429344	429344	type	True	76.3552	63	684	95	below_threshold
Cellulophaga tyrosinoxydans	strain=DSM 21164	GCA_900176415.1	504486	504486	type	True	76.2101	57	684	95	below_threshold
Croceitalea dokdonensis	strain=DOKDO 023	GCA_001306415.1	346188	346188	type	True	76.1539	81	684	95	below_threshold
Maribacter algicola	strain=PoM-212	GCA_003933245.1	2498892	2498892	type	True	76.1031	56	684	95	below_threshold
Poritiphilus flavus	strain=R33	GCA_009901585.1	2697053	2697053	type	True	76.0487	51	684	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 23:07:05,510] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6750/tc_result.tsv
[2023-03-17 23:07:05,510] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:07:05,510] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:07:05,510] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdfdef96c-4f5f-4be8-9523-d93d624cee35/dqc_reference/checkm_data
[2023-03-17 23:07:05,511] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:07:05,515] [INFO] Task started: CheckM
[2023-03-17 23:07:05,515] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6750/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6750/checkm_input OceanDNA-b6750/checkm_result
[2023-03-17 23:07:54,993] [INFO] Task succeeded: CheckM
[2023-03-17 23:07:54,993] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 13.02%
Strain heterogeneity: 25.00%
--------------------------------------------------------------------------------
[2023-03-17 23:07:54,999] [INFO] ===== Completeness check finished =====
[2023-03-17 23:07:54,999] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:07:54,999] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6750/markers.fasta)
[2023-03-17 23:07:55,000] [INFO] Task started: Blastn
[2023-03-17 23:07:55,000] [INFO] Running command: blastn -query OceanDNA-b6750/markers.fasta -db /var/lib/cwl/stgdfdef96c-4f5f-4be8-9523-d93d624cee35/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6750/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:07:55,778] [INFO] Task succeeded: Blastn
[2023-03-17 23:07:55,780] [INFO] Selected 24 target genomes.
[2023-03-17 23:07:55,780] [INFO] Target genome list was writen to OceanDNA-b6750/target_genomes_gtdb.txt
[2023-03-17 23:07:55,812] [INFO] Task started: fastANI
[2023-03-17 23:07:55,812] [INFO] Running command: fastANI --query /var/lib/cwl/stg1afcda53-1816-4e44-b84e-ab8626c872e7/OceanDNA-b6750.fa --refList OceanDNA-b6750/target_genomes_gtdb.txt --output OceanDNA-b6750/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:08:10,779] [INFO] Task succeeded: fastANI
[2023-03-17 23:08:10,792] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 23:08:10,792] [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_005937185.1	s__Muricauda algicola	78.7869	317	684	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129665.1	s__Muricauda flava	78.343	270	684	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014698935.1	s__Muricauda sp014698935	78.0234	195	684	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215465.1	s__Muricauda pacifica_A	78.0167	212	684	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004804315.1	s__Muricauda sp004804315	77.983	213	684	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008040165.1	s__Muricauda hymeniacidonis	77.9654	202	684	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003382275.1	s__Muricauda nanhaiensis	77.8563	182	684	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003149745.1	s__Muricauda koreensis	77.7829	215	684	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010993855.1	s__Muricauda sp010993855	77.776	233	684	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000224085.1	s__Muricauda ruestringensis	77.7417	129	684	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010993815.1	s__Muricauda sp010993815	77.6621	171	684	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009184425.1	s__Muricauda olearia	77.6207	176	684	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	96.52	96.52	0.87	0.87	2	-
GCF_000745185.1	s__Muricauda sp000745185	77.577	173	684	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001683915.1	s__Muricauda sp001683915	77.5659	172	684	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	99.66	99.66	0.95	0.95	2	-
GCF_017313105.1	s__Muricauda sp017313105	77.5649	146	684	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002813125.1	s__Muricauda sp002813125	77.5544	138	684	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003057865.1	s__Muricauda brasiliensis	77.5274	130	684	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	96.90	96.90	0.89	0.89	2	-
GCF_003584135.1	s__Muricauda sp003584135	77.4756	137	684	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	0.99	0.99	2	-
GCA_018222835.1	s__Muricauda sp018222835	77.4232	126	684	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011068285.1	s__Muricauda sp011068285	77.4169	139	684	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018449435.1	s__Muricauda sp018449435	77.3872	160	684	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013090115.1	s__Muricauda amphidinii	77.3328	218	684	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001145.1	s__Croceitalea sp013001145	76.8134	73	684	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Croceitalea	95.0	99.20	99.17	0.87	0.85	5	-
GCF_003148665.1	s__Maribacter_A polysiphoniae	76.3552	63	684	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	99.27	98.55	0.95	0.91	3	-
--------------------------------------------------------------------------------
[2023-03-17 23:08:10,793] [INFO] GTDB search result was written to OceanDNA-b6750/result_gtdb.tsv
[2023-03-17 23:08:10,793] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:08:10,796] [INFO] DFAST_QC result json was written to OceanDNA-b6750/dqc_result.json
[2023-03-17 23:08:10,796] [INFO] DFAST_QC completed!
[2023-03-17 23:08:10,796] [INFO] Total running time: 0h1m42s