[2023-03-18 00:53:42,860] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:53:42,860] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:53:42,860] [INFO] DQC Reference Directory: /var/lib/cwl/stg11c40f29-e0c8-4ff3-a349-57c34824410e/dqc_reference
[2023-03-18 00:53:44,411] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:53:44,411] [INFO] Task started: Prodigal
[2023-03-18 00:53:44,412] [INFO] Running command: cat /var/lib/cwl/stg2e9e10da-ab26-4412-a714-bf21f3041b52/OceanDNA-b29517.fa | prodigal -d OceanDNA-b29517/cds.fna -a OceanDNA-b29517/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:54:11,574] [INFO] Task succeeded: Prodigal
[2023-03-18 00:54:11,574] [INFO] Task started: HMMsearch
[2023-03-18 00:54:11,574] [INFO] Running command: hmmsearch --tblout OceanDNA-b29517/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg11c40f29-e0c8-4ff3-a349-57c34824410e/dqc_reference/reference_markers.hmm OceanDNA-b29517/protein.faa > /dev/null
[2023-03-18 00:54:11,788] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:54:11,788] [INFO] Found 6/6 markers.
[2023-03-18 00:54:11,814] [INFO] Query marker FASTA was written to OceanDNA-b29517/markers.fasta
[2023-03-18 00:54:11,815] [INFO] Task started: Blastn
[2023-03-18 00:54:11,815] [INFO] Running command: blastn -query OceanDNA-b29517/markers.fasta -db /var/lib/cwl/stg11c40f29-e0c8-4ff3-a349-57c34824410e/dqc_reference/reference_markers.fasta -out OceanDNA-b29517/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:54:12,797] [INFO] Task succeeded: Blastn
[2023-03-18 00:54:12,798] [INFO] Selected 31 target genomes.
[2023-03-18 00:54:12,799] [INFO] Target genome list was writen to OceanDNA-b29517/target_genomes.txt
[2023-03-18 00:54:12,815] [INFO] Task started: fastANI
[2023-03-18 00:54:12,815] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e9e10da-ab26-4412-a714-bf21f3041b52/OceanDNA-b29517.fa --refList OceanDNA-b29517/target_genomes.txt --output OceanDNA-b29517/fastani_result.tsv --threads 1
[2023-03-18 00:54:37,112] [INFO] Task succeeded: fastANI
[2023-03-18 00:54:37,112] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg11c40f29-e0c8-4ff3-a349-57c34824410e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:54:37,112] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg11c40f29-e0c8-4ff3-a349-57c34824410e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:54:37,129] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:54:37,129] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 00:54:37,129] [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
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	79.7224	638	1412	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	79.4383	582	1412	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	79.4239	580	1412	95	below_threshold
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	79.258	571	1412	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	79.1954	628	1412	95	below_threshold
Salipiger profundus	strain=JLT2016	GCA_001969385.1	1229727	1229727	type	True	79.1869	598	1412	95	below_threshold
Limimaricola hongkongensis	strain=DSM 17492	GCA_000600975.2	278132	278132	type	True	79.1374	456	1412	95	below_threshold
Limimaricola hongkongensis	strain=UST950701-009P	GCA_000365005.1	278132	278132	type	True	79.0795	466	1412	95	below_threshold
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	78.9361	543	1412	95	below_threshold
Lutimaribacter saemankumensis	strain=DSM 28010	GCA_900100005.1	490829	490829	type	True	78.8902	465	1412	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	78.8853	519	1412	95	below_threshold
Roseovarius indicus	strain=B108	GCA_001441635.1	540747	540747	type	True	78.8258	534	1412	95	below_threshold
Pseudodonghicola xiamenensis	strain=DSM 18339	GCA_000429365.1	337702	337702	type	True	78.8001	512	1412	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_900112725.1	540747	540747	type	True	78.7989	540	1412	95	below_threshold
Pseudodonghicola xiamenensis	strain=CGMCC 1.7081	GCA_014653505.1	337702	337702	type	True	78.7973	513	1412	95	below_threshold
Pseudooceanicola onchidii	strain=XY-99	GCA_004959925.1	2562279	2562279	type	True	78.7814	475	1412	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	78.7805	549	1412	95	below_threshold
Pseudooceanicola marinus	strain=CECT 7751	GCA_900172385.1	396013	396013	type	True	78.7436	487	1412	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	78.7282	491	1412	95	below_threshold
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	78.7231	566	1412	95	below_threshold
Pseudooceanicola nanhaiensis	strain=CGMCC 1.6293	GCA_014645095.1	375761	375761	type	True	78.715	565	1412	95	below_threshold
Limimaricola variabilis	strain=CECT 8572	GCA_014195545.1	1492771	1492771	type	True	78.6565	473	1412	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.4502	449	1412	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	78.3648	481	1412	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.3122	402	1412	95	below_threshold
Sinirhodobacter huangdaonensis	strain=CGMCC 1.12963	GCA_004022465.1	2501515	2501515	type	True	78.2824	470	1412	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	78.2018	452	1412	95	below_threshold
Mangrovicoccus ximenensis	strain=T1lg56	GCA_003056725.1	1911570	1911570	type	True	78.0958	472	1412	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	78.0937	393	1412	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	77.9761	460	1412	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.9616	336	1412	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 00:54:37,129] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29517/tc_result.tsv
[2023-03-18 00:54:37,129] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:54:37,129] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:54:37,129] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg11c40f29-e0c8-4ff3-a349-57c34824410e/dqc_reference/checkm_data
[2023-03-18 00:54:37,130] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:54:37,151] [INFO] Task started: CheckM
[2023-03-18 00:54:37,151] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29517/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29517/checkm_input OceanDNA-b29517/checkm_result
[2023-03-18 00:55:50,875] [INFO] Task succeeded: CheckM
[2023-03-18 00:55:50,876] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:55:50,879] [INFO] ===== Completeness check finished =====
[2023-03-18 00:55:50,879] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:55:50,879] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29517/markers.fasta)
[2023-03-18 00:55:50,880] [INFO] Task started: Blastn
[2023-03-18 00:55:50,880] [INFO] Running command: blastn -query OceanDNA-b29517/markers.fasta -db /var/lib/cwl/stg11c40f29-e0c8-4ff3-a349-57c34824410e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29517/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:55:52,858] [INFO] Task succeeded: Blastn
[2023-03-18 00:55:52,859] [INFO] Selected 22 target genomes.
[2023-03-18 00:55:52,859] [INFO] Target genome list was writen to OceanDNA-b29517/target_genomes_gtdb.txt
[2023-03-18 00:55:52,890] [INFO] Task started: fastANI
[2023-03-18 00:55:52,891] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e9e10da-ab26-4412-a714-bf21f3041b52/OceanDNA-b29517.fa --refList OceanDNA-b29517/target_genomes_gtdb.txt --output OceanDNA-b29517/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:56:12,773] [INFO] Task succeeded: fastANI
[2023-03-18 00:56:12,786] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 00:56:12,786] [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_900109145.1	s__Marinovum algicola	98.9992	1352	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinovum	95.0	99.11	98.22	0.94	0.88	3	conclusive
GCA_006226775.1	s__Marinovum sp006226775	83.7734	873	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinovum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975705.1	s__Salipiger abyssi	80.1917	666	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358185.1	s__Antarcticimicrobium luteum	79.8342	594	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017311415.1	s__Salipiger abyssi_A	79.7604	657	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344785.1	s__Puniceibacterium profundi	79.5854	626	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900184945.1	s__Maliponia aquimaris	79.4854	677	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maliponia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109035.1	s__Cribrihabitans marinus	79.3853	585	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_009789075.1	s__Pseudooceanicola pacificus	79.2774	381	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003511785.1	s__UBA7951 sp003511785	79.2279	403	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA7951	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102075.1	s__Salipiger thiooxidans	79.2035	627	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.34	95.88	0.90	0.85	6	-
GCF_000600975.2	s__Limimaricola hongkongensis	79.117	458	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	99.99	99.99	1.00	1.00	2	-
GCA_001314655.1	s__Salibaculum sp001314655	78.886	531	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013317235.1	s__Leisingera sp013317235	78.8394	550	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429365.1	s__Pseudodonghicola xiamenensis	78.8256	509	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudodonghicola	95.0	99.98	99.98	0.98	0.98	2	-
GCF_000220565.1	s__Pseudooceanicola sp000220565	78.8129	493	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008728195.1	s__Roseovarius indicus	78.7917	546	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.18	97.54	0.97	0.92	4	-
GCF_002786295.1	s__Pseudooceanicola marinus	78.7369	491	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003651245.1	s__Roseovarius spongiae	78.5416	502	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109855.1	s__Roseovarius tolerans	78.4379	492	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.73	96.73	0.86	0.86	2	-
GCF_014903745.1	s__Mangrovicoccus sp014903745	78.2348	449	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005870025.1	s__Mangrovicoccus sp005870025	78.2207	607	1412	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 00:56:12,786] [INFO] GTDB search result was written to OceanDNA-b29517/result_gtdb.tsv
[2023-03-18 00:56:12,786] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:56:12,789] [INFO] DFAST_QC result json was written to OceanDNA-b29517/dqc_result.json
[2023-03-18 00:56:12,789] [INFO] DFAST_QC completed!
[2023-03-18 00:56:12,789] [INFO] Total running time: 0h2m30s