[2023-03-16 07:28:30,037] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:28:30,037] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:28:30,037] [INFO] DQC Reference Directory: /var/lib/cwl/stg7e77718b-bd98-4465-80b9-540652308f8b/dqc_reference
[2023-03-16 07:28:31,150] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:28:31,150] [INFO] Task started: Prodigal
[2023-03-16 07:28:31,151] [INFO] Running command: cat /var/lib/cwl/stg90914f49-05cc-4043-995d-c0ecb7c0a2cb/OceanDNA-b9789.fa | prodigal -d OceanDNA-b9789/cds.fna -a OceanDNA-b9789/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:28:48,569] [INFO] Task succeeded: Prodigal
[2023-03-16 07:28:48,570] [INFO] Task started: HMMsearch
[2023-03-16 07:28:48,570] [INFO] Running command: hmmsearch --tblout OceanDNA-b9789/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7e77718b-bd98-4465-80b9-540652308f8b/dqc_reference/reference_markers.hmm OceanDNA-b9789/protein.faa > /dev/null
[2023-03-16 07:28:48,736] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:28:48,737] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg90914f49-05cc-4043-995d-c0ecb7c0a2cb/OceanDNA-b9789.fa]
[2023-03-16 07:28:48,758] [INFO] Query marker FASTA was written to OceanDNA-b9789/markers.fasta
[2023-03-16 07:28:48,759] [INFO] Task started: Blastn
[2023-03-16 07:28:48,759] [INFO] Running command: blastn -query OceanDNA-b9789/markers.fasta -db /var/lib/cwl/stg7e77718b-bd98-4465-80b9-540652308f8b/dqc_reference/reference_markers.fasta -out OceanDNA-b9789/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:28:49,295] [INFO] Task succeeded: Blastn
[2023-03-16 07:28:49,297] [INFO] Selected 16 target genomes.
[2023-03-16 07:28:49,297] [INFO] Target genome list was writen to OceanDNA-b9789/target_genomes.txt
[2023-03-16 07:28:49,309] [INFO] Task started: fastANI
[2023-03-16 07:28:49,310] [INFO] Running command: fastANI --query /var/lib/cwl/stg90914f49-05cc-4043-995d-c0ecb7c0a2cb/OceanDNA-b9789.fa --refList OceanDNA-b9789/target_genomes.txt --output OceanDNA-b9789/fastani_result.tsv --threads 1
[2023-03-16 07:28:59,107] [INFO] Task succeeded: fastANI
[2023-03-16 07:28:59,107] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7e77718b-bd98-4465-80b9-540652308f8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:28:59,108] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7e77718b-bd98-4465-80b9-540652308f8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:28:59,117] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 07:28:59,117] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 07:28:59,118] [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 pacifica	strain=DSM 25027	GCA_003001695.1	1080225	1080225	type	True	79.2461	382	682	95	below_threshold
Muricauda hymeniacidonis	strain=176CP4-71	GCA_004296335.1	2517819	2517819	type	True	77.0846	191	682	95	below_threshold
Muricauda nanhaiensis	strain=SM1704	GCA_003382275.1	2292706	2292706	type	True	77.0702	141	682	95	below_threshold
Muricauda flava	strain=DSM 22638	GCA_900129665.1	570519	570519	type	True	77.0049	135	682	95	below_threshold
Muricauda parva	strain=DSM 25885	GCA_900215465.1	1247520	1247520	type	True	76.9867	161	682	95	below_threshold
Muricauda amphidinii	strain=LMIT004	GCA_013090115.1	2735167	2735167	type	True	76.959	166	682	95	below_threshold
Muricauda aequoris	strain=NH166	GCA_003584165.1	2306997	2306997	type	True	76.8759	105	682	95	below_threshold
Muricauda aequoris	strain=NH166	GCA_008017345.1	2306997	2306997	type	True	76.8759	105	682	95	below_threshold
Muricauda zhangzhouensis	strain=DSM 25030	GCA_900106825.1	1073328	1073328	type	True	76.8345	139	682	95	below_threshold
Muricauda zhangzhouensis	strain=CGMCC 1.11028	GCA_900102925.1	1073328	1073328	type	True	76.8039	139	682	95	below_threshold
Muricauda maritima	strain=72	GCA_003584135.1	2306998	2306998	type	True	76.7624	115	682	95	below_threshold
Muricauda aurea	strain=BC31-1-A7	GCA_017313785.1	2915619	2915619	type	True	76.6309	101	682	95	below_threshold
Muricauda beolgyonensis	strain=KCTC 23501	GCA_003992615.1	864064	864064	type	True	76.4187	119	682	95	below_threshold
Muricauda aurantiaca	strain=HME9304	GCA_003269425.1	1383885	1383885	type	True	76.3954	129	682	95	below_threshold
Arenibacter palladensis	strain=DSM 17539	GCA_900129275.1	237373	237373	type	True	75.7145	54	682	95	below_threshold
Arenibacter troitsensis	strain=DSM 19835	GCA_900177645.1	188872	188872	type	True	75.6833	50	682	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 07:28:59,119] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9789/tc_result.tsv
[2023-03-16 07:28:59,119] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:28:59,119] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:28:59,119] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7e77718b-bd98-4465-80b9-540652308f8b/dqc_reference/checkm_data
[2023-03-16 07:28:59,120] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:28:59,136] [INFO] Task started: CheckM
[2023-03-16 07:28:59,137] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9789/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9789/checkm_input OceanDNA-b9789/checkm_result
[2023-03-16 07:29:46,192] [INFO] Task succeeded: CheckM
[2023-03-16 07:29:46,193] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 07:29:46,196] [INFO] ===== Completeness check finished =====
[2023-03-16 07:29:46,196] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:29:46,197] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9789/markers.fasta)
[2023-03-16 07:29:46,198] [INFO] Task started: Blastn
[2023-03-16 07:29:46,198] [INFO] Running command: blastn -query OceanDNA-b9789/markers.fasta -db /var/lib/cwl/stg7e77718b-bd98-4465-80b9-540652308f8b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9789/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:29:47,054] [INFO] Task succeeded: Blastn
[2023-03-16 07:29:47,055] [INFO] Selected 17 target genomes.
[2023-03-16 07:29:47,056] [INFO] Target genome list was writen to OceanDNA-b9789/target_genomes_gtdb.txt
[2023-03-16 07:29:47,218] [INFO] Task started: fastANI
[2023-03-16 07:29:47,218] [INFO] Running command: fastANI --query /var/lib/cwl/stg90914f49-05cc-4043-995d-c0ecb7c0a2cb/OceanDNA-b9789.fa --refList OceanDNA-b9789/target_genomes_gtdb.txt --output OceanDNA-b9789/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:29:58,438] [INFO] Task succeeded: fastANI
[2023-03-16 07:29:58,448] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 07:29:58,448] [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_003001695.1	s__Muricauda pacifica	79.2461	382	682	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004296335.1	s__Muricauda sp004296335	77.0716	192	682	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	77.0345	143	682	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	77.0049	135	682	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	77.0025	160	682	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	76.9737	148	682	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	76.959	166	682	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003584165.1	s__Muricauda sp003584165	76.8759	105	682	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900102925.1	s__Muricauda zhangzhouensis	76.8039	139	682	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003584135.1	s__Muricauda sp003584135	76.7624	115	682	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	0.99	0.99	2	-
GCF_017313785.1	s__Muricauda sp002711825	76.6309	101	682	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	98.76	98.31	0.81	0.77	4	-
GCF_008040165.1	s__Muricauda hymeniacidonis	76.5743	152	682	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	76.4553	151	682	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	76.4538	153	682	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003992615.1	s__Muricauda beolgyonensis	76.4187	119	682	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003269425.1	s__Muricauda maritima	76.3954	129	682	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148665.1	s__Maribacter_A polysiphoniae	75.681	60	682	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	99.27	98.55	0.95	0.91	3	-
--------------------------------------------------------------------------------
[2023-03-16 07:29:58,448] [INFO] GTDB search result was written to OceanDNA-b9789/result_gtdb.tsv
[2023-03-16 07:29:58,448] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:29:58,450] [INFO] DFAST_QC result json was written to OceanDNA-b9789/dqc_result.json
[2023-03-16 07:29:58,450] [INFO] DFAST_QC completed!
[2023-03-16 07:29:58,450] [INFO] Total running time: 0h1m28s