[2023-03-16 06:50:39,212] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:50:39,212] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:50:39,213] [INFO] DQC Reference Directory: /var/lib/cwl/stgd5ad295d-7b0f-4c42-a0d8-64ff1a2a990b/dqc_reference
[2023-03-16 06:50:40,296] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:50:40,296] [INFO] Task started: Prodigal
[2023-03-16 06:50:40,297] [INFO] Running command: cat /var/lib/cwl/stgf1177a20-eb9a-42e5-98ef-09257b49f5d5/OceanDNA-b27575.fa | prodigal -d OceanDNA-b27575/cds.fna -a OceanDNA-b27575/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:50:56,677] [INFO] Task succeeded: Prodigal
[2023-03-16 06:50:56,677] [INFO] Task started: HMMsearch
[2023-03-16 06:50:56,677] [INFO] Running command: hmmsearch --tblout OceanDNA-b27575/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd5ad295d-7b0f-4c42-a0d8-64ff1a2a990b/dqc_reference/reference_markers.hmm OceanDNA-b27575/protein.faa > /dev/null
[2023-03-16 06:50:56,865] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:50:56,866] [INFO] Found 6/6 markers.
[2023-03-16 06:50:56,891] [INFO] Query marker FASTA was written to OceanDNA-b27575/markers.fasta
[2023-03-16 06:50:56,892] [INFO] Task started: Blastn
[2023-03-16 06:50:56,893] [INFO] Running command: blastn -query OceanDNA-b27575/markers.fasta -db /var/lib/cwl/stgd5ad295d-7b0f-4c42-a0d8-64ff1a2a990b/dqc_reference/reference_markers.fasta -out OceanDNA-b27575/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:50:57,800] [INFO] Task succeeded: Blastn
[2023-03-16 06:50:57,802] [INFO] Selected 30 target genomes.
[2023-03-16 06:50:57,802] [INFO] Target genome list was writen to OceanDNA-b27575/target_genomes.txt
[2023-03-16 06:50:57,829] [INFO] Task started: fastANI
[2023-03-16 06:50:57,829] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1177a20-eb9a-42e5-98ef-09257b49f5d5/OceanDNA-b27575.fa --refList OceanDNA-b27575/target_genomes.txt --output OceanDNA-b27575/fastani_result.tsv --threads 1
[2023-03-16 06:51:17,628] [INFO] Task succeeded: fastANI
[2023-03-16 06:51:17,629] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd5ad295d-7b0f-4c42-a0d8-64ff1a2a990b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 06:51:17,629] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd5ad295d-7b0f-4c42-a0d8-64ff1a2a990b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 06:51:17,644] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 06:51:17,644] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 06:51:17,644] [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
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	78.9018	480	873	95	below_threshold
Limimaricola hongkongensis	strain=DSM 17492	GCA_000600975.2	278132	278132	type	True	78.3018	308	873	95	below_threshold
Limimaricola hongkongensis	strain=UST950701-009P	GCA_000365005.1	278132	278132	type	True	78.2278	311	873	95	below_threshold
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	78.1892	329	873	95	below_threshold
Limimaricola soesokkakensis	strain=DSM 29956	GCA_003014435.1	1343159	1343159	type	True	77.8961	290	873	95	below_threshold
Limimaricola soesokkakensis	strain=CECT 8367	GCA_900172345.1	1343159	1343159	type	True	77.8326	298	873	95	below_threshold
Salibaculum halophilum	strain=WDS1C4	GCA_002094885.1	1914408	1914408	type	True	77.8232	241	873	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000379485.1	390641	390641	type	True	77.7382	309	873	95	below_threshold
Wenxinia marina	strain=CGMCC 1.6105	GCA_014645075.1	390641	390641	type	True	77.7337	310	873	95	below_threshold
Wenxinia saemankumensis	strain=DSM 100565	GCA_900141735.1	1447782	1447782	type	True	77.7216	314	873	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000836695.1	390641	390641	type	True	77.712	313	873	95	below_threshold
Limimaricola variabilis	strain=CECT 8572	GCA_014195545.1	1492771	1492771	type	True	77.6648	288	873	95	below_threshold
Rhodovulum robiginosum	strain=DSM 12329	GCA_003944755.1	68292	68292	type	True	77.5777	262	873	95	below_threshold
Limimaricola cinnabarinus	strain=LL-001	GCA_000466965.1	1125964	1125964	type	True	77.4637	286	873	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.3462	240	873	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	77.3175	214	873	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	77.1946	278	873	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	77.1711	284	873	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	77.0034	238	873	95	below_threshold
Sulfitobacter sabulilitoris	strain=HSMS-29	GCA_005887615.1	2562655	2562655	type	True	76.9786	226	873	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	76.9752	207	873	95	below_threshold
Paracoccus salsus	strain=EGI L200073	GCA_021556615.1	2911061	2911061	type	True	76.787	132	873	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	76.5016	187	873	95	below_threshold
Pelagivirga dicentrarchi	strain=YLY04	GCA_003316635.1	2250573	2250573	type	True	76.4689	181	873	95	below_threshold
Sagittula marina	strain=DSM 102235	GCA_014196795.1	943940	943940	type	True	75.9205	126	873	95	below_threshold
Nocardia transvalensis	strain=DSM 43582	GCA_014203315.1	37333	37333	type	True	74.622	63	873	95	below_threshold
Nocardia transvalensis	strain=NBRC 15921	GCA_000308875.1	37333	37333	type	True	74.6187	64	873	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 06:51:17,645] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27575/tc_result.tsv
[2023-03-16 06:51:17,645] [INFO] ===== Taxonomy check completed =====
[2023-03-16 06:51:17,645] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:51:17,645] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd5ad295d-7b0f-4c42-a0d8-64ff1a2a990b/dqc_reference/checkm_data
[2023-03-16 06:51:17,646] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:51:17,913] [INFO] Task started: CheckM
[2023-03-16 06:51:17,913] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27575/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27575/checkm_input OceanDNA-b27575/checkm_result
[2023-03-16 06:52:00,281] [INFO] Task succeeded: CheckM
[2023-03-16 06:52:00,281] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.38%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 06:52:00,287] [INFO] ===== Completeness check finished =====
[2023-03-16 06:52:00,287] [INFO] ===== Start GTDB Search =====
[2023-03-16 06:52:00,287] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27575/markers.fasta)
[2023-03-16 06:52:00,288] [INFO] Task started: Blastn
[2023-03-16 06:52:00,289] [INFO] Running command: blastn -query OceanDNA-b27575/markers.fasta -db /var/lib/cwl/stgd5ad295d-7b0f-4c42-a0d8-64ff1a2a990b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27575/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:52:01,891] [INFO] Task succeeded: Blastn
[2023-03-16 06:52:01,895] [INFO] Selected 34 target genomes.
[2023-03-16 06:52:01,895] [INFO] Target genome list was writen to OceanDNA-b27575/target_genomes_gtdb.txt
[2023-03-16 06:52:02,070] [INFO] Task started: fastANI
[2023-03-16 06:52:02,070] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1177a20-eb9a-42e5-98ef-09257b49f5d5/OceanDNA-b27575.fa --refList OceanDNA-b27575/target_genomes_gtdb.txt --output OceanDNA-b27575/fastani_result_gtdb.tsv --threads 1
[2023-03-16 06:52:24,609] [INFO] Task succeeded: fastANI
[2023-03-16 06:52:24,625] [INFO] Found 30 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 06:52:24,626] [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_004000435.1	s__Flavimaricola sp004000435	78.9109	479	873	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Flavimaricola	95.0	99.99	99.97	0.99	0.98	36	-
GCF_000600975.2	s__Limimaricola hongkongensis	78.2967	309	873	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900102015.1	s__Limimaricola pyoseonensis	78.2342	325	873	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002723615.1	s__Limimaricola cinnabarinus_B	78.0795	322	873	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006226775.1	s__Marinovum sp006226775	78.0017	350	873	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinovum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009993005.1	s__JAACUH01 sp009993005	77.9956	360	873	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAACUH01	95.0	99.57	99.57	0.91	0.91	2	-
GCF_000153305.1	s__Oceanicola granulosus	77.9649	328	873	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001314655.1	s__Salibaculum sp001314655	77.9114	320	873	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172345.1	s__Limimaricola soesokkakensis	77.8903	293	873	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002094885.1	s__Salibaculum halophilum	77.8095	242	873	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001482405.1	s__Ponticoccus marisrubri	77.7974	354	873	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ponticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172235.1	s__Pseudoruegeria aquimaris	77.7913	280	873	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudoruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379485.1	s__Wenxinia marina	77.7602	307	873	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wenxinia	95.0	99.99	99.99	0.99	0.99	3	-
GCF_900141735.1	s__Wenxinia saemankumensis	77.7323	313	873	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wenxinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014195545.1	s__Limimaricola variabilis	77.6657	288	873	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003944755.1	s__Rhodovulum robiginosum	77.5889	261	873	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004145405.1	s__Loktanella sp004145405	77.5036	267	873	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002814095.1	s__Sagittula sp002814095	77.4337	268	873	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975705.1	s__Salipiger abyssi	77.405	307	873	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003053725.1	s__Rhodovulum kholense	77.3335	255	873	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	98.27	98.27	0.96	0.96	2	-
GCF_900116005.1	s__Poseidonocella sedimentorum	77.3185	238	873	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Poseidonocella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003072125.1	s__Roseovarius sediminicola	77.2925	216	873	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003667315.2	s__Tropicibacter sp003667315	77.2032	262	873	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000521865.1	s__Roseivivax isoporae	77.1807	283	873	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001687105.1	s__Salipiger sp001687105	77.0504	274	873	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	96.47	96.47	0.82	0.82	2	-
GCA_018222585.1	s__Pseudooceanicola sp018222585	76.9415	243	873	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.94	99.94	0.96	0.96	2	-
GCA_013003075.1	s__IMCC34051 sp013003075	76.9127	142	873	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__IMCC34051	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129395.1	s__Ascidiaceihabitans pseudonitzschiae	76.5089	185	873	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
GCF_003316635.1	s__Roseovarius dicentrarchi	76.469	181	873	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013377085.1	s__Rhodoplanes sp013377085	75.0101	83	873	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 06:52:24,629] [INFO] GTDB search result was written to OceanDNA-b27575/result_gtdb.tsv
[2023-03-16 06:52:24,634] [INFO] ===== GTDB Search completed =====
[2023-03-16 06:52:24,639] [INFO] DFAST_QC result json was written to OceanDNA-b27575/dqc_result.json
[2023-03-16 06:52:24,639] [INFO] DFAST_QC completed!
[2023-03-16 06:52:24,639] [INFO] Total running time: 0h1m45s