[2023-03-15 06:07:05,832] [INFO] DFAST_QC pipeline started.
[2023-03-15 06:07:05,834] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 06:07:05,834] [INFO] DQC Reference Directory: /var/lib/cwl/stgf23370c3-a975-42c6-8424-8c202a2e07e6/dqc_reference
[2023-03-15 06:07:10,445] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 06:07:10,446] [INFO] Task started: Prodigal
[2023-03-15 06:07:10,446] [INFO] Running command: cat /var/lib/cwl/stg9f7166da-3b4e-4ce4-9384-5d468da3177e/OceanDNA-b32895.fa | prodigal -d OceanDNA-b32895/cds.fna -a OceanDNA-b32895/protein.faa -g 11 -q > /dev/null
[2023-03-15 06:07:25,131] [INFO] Task succeeded: Prodigal
[2023-03-15 06:07:25,132] [INFO] Task started: HMMsearch
[2023-03-15 06:07:25,132] [INFO] Running command: hmmsearch --tblout OceanDNA-b32895/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf23370c3-a975-42c6-8424-8c202a2e07e6/dqc_reference/reference_markers.hmm OceanDNA-b32895/protein.faa > /dev/null
[2023-03-15 06:07:25,403] [INFO] Task succeeded: HMMsearch
[2023-03-15 06:07:25,404] [INFO] Found 6/6 markers.
[2023-03-15 06:07:25,484] [INFO] Query marker FASTA was written to OceanDNA-b32895/markers.fasta
[2023-03-15 06:07:25,507] [INFO] Task started: Blastn
[2023-03-15 06:07:25,508] [INFO] Running command: blastn -query OceanDNA-b32895/markers.fasta -db /var/lib/cwl/stgf23370c3-a975-42c6-8424-8c202a2e07e6/dqc_reference/reference_markers.fasta -out OceanDNA-b32895/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 06:07:29,521] [INFO] Task succeeded: Blastn
[2023-03-15 06:07:29,529] [INFO] Selected 28 target genomes.
[2023-03-15 06:07:29,529] [INFO] Target genome list was writen to OceanDNA-b32895/target_genomes.txt
[2023-03-15 06:07:29,569] [INFO] Task started: fastANI
[2023-03-15 06:07:29,570] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f7166da-3b4e-4ce4-9384-5d468da3177e/OceanDNA-b32895.fa --refList OceanDNA-b32895/target_genomes.txt --output OceanDNA-b32895/fastani_result.tsv --threads 1
[2023-03-15 06:07:49,627] [INFO] Task succeeded: fastANI
[2023-03-15 06:07:49,628] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf23370c3-a975-42c6-8424-8c202a2e07e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 06:07:49,628] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf23370c3-a975-42c6-8424-8c202a2e07e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 06:07:49,644] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 06:07:49,644] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 06:07:49,644] [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
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	76.5272	171	822	95	below_threshold
Hypericibacter terrae	strain=R5913	GCA_008728855.1	2602015	2602015	type	True	76.4258	168	822	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	76.401	143	822	95	below_threshold
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	76.3659	109	822	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	76.3471	116	822	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.3394	206	822	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	76.3337	209	822	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	76.2287	128	822	95	below_threshold
Skermanella pratensis	strain=W17	GCA_008843145.1	2233999	2233999	type	True	76.2227	130	822	95	below_threshold
Telmatospirillum siberiense	strain=26-4b1	GCA_002845745.1	382514	382514	type	True	76.2142	85	822	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	76.1255	121	822	95	below_threshold
Magnetospirillum marisnigri	strain=SP-1	GCA_001650715.1	1285242	1285242	type	True	76.1005	118	822	95	below_threshold
Skermanella mucosa	strain=KEMB 2255-438	GCA_016765655.2	1789672	1789672	type	True	76.0417	154	822	95	below_threshold
Methyloligella halotolerans	strain=VKM B-2706	GCA_001708935.1	1177755	1177755	type	True	76.0199	63	822	95	below_threshold
Brevundimonas bacteroides	strain=DSM 4726	GCA_000701445.1	74311	74311	type	True	76.0182	60	822	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_014197785.1	34017	34017	type	True	75.9946	114	822	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_016653375.1	34017	34017	type	True	75.982	115	822	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_003258835.1	34017	34017	type	True	75.9757	112	822	95	below_threshold
Nitrospirillum iridis	strain=DSM 22198	GCA_014205765.1	765888	765888	type	True	75.9193	109	822	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	75.8834	108	822	95	below_threshold
Oceanicella actignis	strain=DSM 22673	GCA_008124525.1	1189325	1189325	type	True	75.8425	125	822	95	below_threshold
Pleomorphomonas oryzae	strain=DSM 16300	GCA_000422965.1	261934	261934	type	True	75.8384	65	822	95	below_threshold
Rhizomicrobium electricum	strain=DSM 21034	GCA_011762045.1	480070	480070	type	True	75.7667	79	822	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	75.7662	82	822	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	75.7583	113	822	95	below_threshold
Paroceanicella profunda	strain=D4M1	GCA_005887635.2	2579971	2579971	type	True	75.7262	109	822	95	below_threshold
Methylobacterium soli	strain=KCTC 22810	GCA_022179555.1	553447	553447	type	True	75.6593	78	822	95	below_threshold
Methylobacterium jeotgali	strain=LMG 23639	GCA_022179345.1	381630	381630	type	True	75.6	94	822	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 06:07:49,653] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32895/tc_result.tsv
[2023-03-15 06:07:49,667] [INFO] ===== Taxonomy check completed =====
[2023-03-15 06:07:49,667] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 06:07:49,667] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf23370c3-a975-42c6-8424-8c202a2e07e6/dqc_reference/checkm_data
[2023-03-15 06:07:49,668] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 06:07:49,689] [INFO] Task started: CheckM
[2023-03-15 06:07:49,689] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32895/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32895/checkm_input OceanDNA-b32895/checkm_result
[2023-03-15 06:08:31,021] [INFO] Task succeeded: CheckM
[2023-03-15 06:08:31,022] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 06:08:31,193] [INFO] ===== Completeness check finished =====
[2023-03-15 06:08:31,193] [INFO] ===== Start GTDB Search =====
[2023-03-15 06:08:31,194] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32895/markers.fasta)
[2023-03-15 06:08:31,195] [INFO] Task started: Blastn
[2023-03-15 06:08:31,195] [INFO] Running command: blastn -query OceanDNA-b32895/markers.fasta -db /var/lib/cwl/stgf23370c3-a975-42c6-8424-8c202a2e07e6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32895/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 06:08:32,594] [INFO] Task succeeded: Blastn
[2023-03-15 06:08:32,610] [INFO] Selected 33 target genomes.
[2023-03-15 06:08:32,610] [INFO] Target genome list was writen to OceanDNA-b32895/target_genomes_gtdb.txt
[2023-03-15 06:08:32,648] [INFO] Task started: fastANI
[2023-03-15 06:08:32,648] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f7166da-3b4e-4ce4-9384-5d468da3177e/OceanDNA-b32895.fa --refList OceanDNA-b32895/target_genomes_gtdb.txt --output OceanDNA-b32895/fastani_result_gtdb.tsv --threads 1
[2023-03-15 06:08:55,033] [INFO] Task succeeded: fastANI
[2023-03-15 06:08:55,051] [INFO] Found 33 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 06:08:55,051] [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
GCA_016183945.1	s__CAJANL01 sp016183945	76.9748	59	822	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__CAJANL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015232485.1	s__JADFZP01 sp015232485	76.9679	119	822	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__JADFZP01	95.0	96.70	95.97	0.70	0.69	3	-
GCA_009377535.1	s__WHTV01 sp009377535	76.6048	158	822	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__WHTV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008728835.1	s__Hypericibacter adhaerens	76.5254	170	822	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__Hypericibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576685.1	s__SYSU-D60014 sp003576685	76.5075	146	822	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__SYSU-D60014	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008728855.1	s__Hypericibacter terrae	76.4484	166	822	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__Hypericibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000518365.1	s__URHD0088 sp000518365	76.4423	188	822	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__URHD0088	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869675.1	s__VGDP01 sp016869675	76.4369	144	822	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SP197;f__SP197;g__VGDP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004356985.1	s__SMXQ01 sp004356985	76.4005	80	822	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SMXQ01;f__SMXQ01;g__SMXQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904705.1	s__Nisaea sp014904705	76.3759	107	822	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377445.1	s__WHUA01 sp009377445	76.372	99	822	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__UBA8366;g__WHUA01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000299935.1	s__Oceanibaculum indicum	76.3602	115	822	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	97.37	97.37	0.93	0.93	2	-
GCA_011523425.1	s__WTGU01 sp011523425	76.3547	111	822	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA828;f__UBA828;g__WTGU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177295.1	s__Tistlia consotensis	76.3255	210	822	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Tistlia	95.0	99.99	99.99	0.99	0.99	2	-
GCA_018699755.1	s__JABIRQ01 sp018699755	76.2942	99	822	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CADEGL01;f__CADEGL01;g__JABIRQ01	95.0	98.91	98.91	0.81	0.81	2	-
GCA_013349665.1	s__Telmatospirillum sp013349665	76.2556	103	822	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Telmatospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002239065.1	s__MPNO01 sp002239065	76.2185	132	822	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__MPNO01;g__MPNO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016699855.1	s__GCA-016699855 sp016699855	76.2007	139	822	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__GCA-016699855	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650715.1	s__Phaeospirillum marisnigri	76.1152	117	822	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377375.1	s__WHUE01 sp009377375	76.1078	119	822	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA2964;g__WHUE01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197915.1	s__Rhodospira visakhapatnamensis	76.0796	118	822	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017640745.1	s__Nisaea sp017640745	76.0778	115	822	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900184795.1	s__Phaeospirillum sp900184795	76.0607	137	822	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826935.1	s__CADEGR01 sp902826935	76.0488	127	822	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Geminicoccales;f__Geminicoccaceae;g__CADEGR01	95.0	98.81	98.69	0.93	0.92	4	-
GCF_003258835.1	s__Rhodobium orientis	75.9757	112	822	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhodobiaceae;g__Rhodobium	95.0	99.99	99.98	0.99	0.98	3	-
GCA_016869415.1	s__VGEI01 sp016869415	75.9661	86	822	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CACIAM-22H2;f__CACIAM-22H2;g__VGEI01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001014615.2	s__Aquamicrobium_A sp001014615	75.9567	85	822	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003173715.1	s__Methylobacterium durans	75.8385	73	822	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011762045.1	s__Rhizomicrobium electricum	75.7981	77	822	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micropepsales;f__Micropepsaceae;g__Rhizomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005887635.2	s__Paroceanicella profunda	75.7506	107	822	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paroceanicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002355515.1	s__Methylobacterium populi_A	75.5731	100	822	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019241915.1	s__AP-15 sp019241915	75.5726	66	822	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__AP-15	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112625.1	s__Methylobacterium sp900112625	75.3873	98	822	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.34	98.23	0.93	0.92	9	-
--------------------------------------------------------------------------------
[2023-03-15 06:08:55,057] [INFO] GTDB search result was written to OceanDNA-b32895/result_gtdb.tsv
[2023-03-15 06:08:55,066] [INFO] ===== GTDB Search completed =====
[2023-03-15 06:08:55,074] [INFO] DFAST_QC result json was written to OceanDNA-b32895/dqc_result.json
[2023-03-15 06:08:55,074] [INFO] DFAST_QC completed!
[2023-03-15 06:08:55,074] [INFO] Total running time: 0h1m49s