[2023-03-15 16:03:34,273] [INFO] DFAST_QC pipeline started.
[2023-03-15 16:03:34,274] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 16:03:34,274] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb09c4b8-9372-407f-a638-163ede536df6/dqc_reference
[2023-03-15 16:03:35,750] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 16:03:35,750] [INFO] Task started: Prodigal
[2023-03-15 16:03:35,751] [INFO] Running command: cat /var/lib/cwl/stg9cf3637b-4736-4336-a10d-c5dc000d5785/OceanDNA-b39298.fa | prodigal -d OceanDNA-b39298/cds.fna -a OceanDNA-b39298/protein.faa -g 11 -q > /dev/null
[2023-03-15 16:03:57,867] [INFO] Task succeeded: Prodigal
[2023-03-15 16:03:57,868] [INFO] Task started: HMMsearch
[2023-03-15 16:03:57,868] [INFO] Running command: hmmsearch --tblout OceanDNA-b39298/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb09c4b8-9372-407f-a638-163ede536df6/dqc_reference/reference_markers.hmm OceanDNA-b39298/protein.faa > /dev/null
[2023-03-15 16:03:58,072] [INFO] Task succeeded: HMMsearch
[2023-03-15 16:03:58,073] [INFO] Found 6/6 markers.
[2023-03-15 16:03:58,095] [INFO] Query marker FASTA was written to OceanDNA-b39298/markers.fasta
[2023-03-15 16:03:58,095] [INFO] Task started: Blastn
[2023-03-15 16:03:58,095] [INFO] Running command: blastn -query OceanDNA-b39298/markers.fasta -db /var/lib/cwl/stgbb09c4b8-9372-407f-a638-163ede536df6/dqc_reference/reference_markers.fasta -out OceanDNA-b39298/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:03:58,759] [INFO] Task succeeded: Blastn
[2023-03-15 16:03:58,761] [INFO] Selected 34 target genomes.
[2023-03-15 16:03:58,761] [INFO] Target genome list was writen to OceanDNA-b39298/target_genomes.txt
[2023-03-15 16:03:58,783] [INFO] Task started: fastANI
[2023-03-15 16:03:58,783] [INFO] Running command: fastANI --query /var/lib/cwl/stg9cf3637b-4736-4336-a10d-c5dc000d5785/OceanDNA-b39298.fa --refList OceanDNA-b39298/target_genomes.txt --output OceanDNA-b39298/fastani_result.tsv --threads 1
[2023-03-15 16:04:23,159] [INFO] Task succeeded: fastANI
[2023-03-15 16:04:23,159] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb09c4b8-9372-407f-a638-163ede536df6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 16:04:23,160] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb09c4b8-9372-407f-a638-163ede536df6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 16:04:23,177] [INFO] Found 34 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 16:04:23,178] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 16:04:23,178] [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
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	77.1058	160	1120	95	below_threshold
Parahaliea maris	strain=HSLHS9	GCA_008064665.1	2716870	2716870	type	True	76.9033	166	1120	95	below_threshold
Pseudomonas sagittaria	strain=JCM 18195	GCA_900115715.1	1135990	1135990	type	True	76.8919	184	1120	95	below_threshold
Microbulbifer rhizosphaerae	strain=CECT 8799	GCA_014191725.1	1562603	1562603	type	True	76.8906	162	1120	95	below_threshold
Parahaliea mediterranea	strain=DSM 21924	GCA_003402235.1	651086	651086	type	True	76.851	182	1120	95	below_threshold
Halomonas shengliensis	strain=CGMCC 1.6444	GCA_900104135.1	419597	419597	type	True	76.8391	201	1120	95	below_threshold
Seongchinamella sediminis	strain=U0301	GCA_003457605.1	2283635	2283635	type	True	76.7563	126	1120	95	below_threshold
Azotobacter chroococcum subsp. isscasi	strain=P205	GCA_004327895.1	2528971	353	type	True	76.7435	168	1120	95	below_threshold
Parahaliea aestuarii	strain=S2-26	GCA_008064635.1	1852021	1852021	type	True	76.7135	174	1120	95	below_threshold
Pseudomonas rhizoryzae	strain=RY24	GCA_005250615.1	2571129	2571129	type	True	76.6677	141	1120	95	below_threshold
Halomonas lactosivorans	strain=KCTC 52281	GCA_003254665.1	2185141	2185141	type	True	76.6489	143	1120	95	below_threshold
Pseudomonas alcaligenes	strain=NCTC10367	GCA_900455475.1	43263	43263	type	True	76.6375	149	1120	95	below_threshold
Halomonas heilongjiangensis	strain=9-2	GCA_003202165.1	1387883	1387883	type	True	76.6325	174	1120	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_013697085.1	321266	321266	type	True	76.5868	128	1120	95	below_threshold
Pseudomonas delhiensis	strain=RLD-1	GCA_900187975.1	366289	366289	type	True	76.5844	221	1120	95	below_threshold
Stutzerimonas azotifigens	strain=DSM 17556	GCA_000425625.1	291995	291995	type	True	76.5835	167	1120	95	below_threshold
Pseudomonas delhiensis	strain=CCM 7361	GCA_900099945.1	366289	366289	type	True	76.5691	221	1120	95	below_threshold
Microbulbifer donghaiensis	strain=CGMCC 1.7063	GCA_900129095.1	494016	494016	type	True	76.5581	134	1120	95	below_threshold
Pseudomaricurvus alcaniphilus	strain=MEBiC06469	GCA_011440395.1	1166482	1166482	type	True	76.43	135	1120	95	below_threshold
[Pseudomonas] nosocomialis	strain=A31/70	GCA_005876855.1	1056496	1056496	type	True	76.3664	140	1120	95	below_threshold
Pseudomonas alcaliphila	strain=JCM 10630	GCA_900101755.1	101564	101564	type	True	76.2737	129	1120	95	below_threshold
Stutzerimonas balearica	strain=DSM 6083	GCA_900103375.1	74829	74829	type	True	76.2718	124	1120	95	below_threshold
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	76.267	112	1120	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_024448335.1	2968969	2968969	type	True	76.2616	114	1120	95	below_threshold
Stutzerimonas balearica	strain=DSM6083 (=SP1402)	GCA_000818015.1	74829	74829	type	True	76.2607	126	1120	95	below_threshold
Pseudomonas alcaliphila	strain=NBRC 102411	GCA_002091495.1	101564	101564	type	True	76.2576	129	1120	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	76.2498	115	1120	95	below_threshold
Chromohalobacter marismortui	strain=DSM 6770	GCA_004364315.1	42055	42055	type	True	76.2439	52	1120	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	76.2199	151	1120	95	below_threshold
Pseudomonas soli	strain=LMG 27941	GCA_900110655.1	1306993	1306993	type	True	76.1353	122	1120	95	below_threshold
Pseudomonas maumuensis	strain=COW77	GCA_019139675.1	2842354	2842354	type	True	76.0974	132	1120	95	below_threshold
Pseudomonas songnenensis	strain=NEAU-ST5-5	GCA_003696315.1	1176259	1176259	type	True	76.0568	102	1120	95	below_threshold
Marinobacterium aestuarii	strain=ST58-10	GCA_001651805.1	1821621	1821621	type	True	75.7265	85	1120	95	below_threshold
Motiliproteus sediminis	strain=HS6	GCA_017912535.1	1468178	1468178	type	True	75.5397	58	1120	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 16:04:23,178] [INFO] DFAST Taxonomy check result was written to OceanDNA-b39298/tc_result.tsv
[2023-03-15 16:04:23,179] [INFO] ===== Taxonomy check completed =====
[2023-03-15 16:04:23,179] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 16:04:23,179] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb09c4b8-9372-407f-a638-163ede536df6/dqc_reference/checkm_data
[2023-03-15 16:04:23,180] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 16:04:23,200] [INFO] Task started: CheckM
[2023-03-15 16:04:23,200] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b39298/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b39298/checkm_input OceanDNA-b39298/checkm_result
[2023-03-15 16:05:17,949] [INFO] Task succeeded: CheckM
[2023-03-15 16:05:17,949] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 16:05:17,954] [INFO] ===== Completeness check finished =====
[2023-03-15 16:05:17,954] [INFO] ===== Start GTDB Search =====
[2023-03-15 16:05:17,955] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b39298/markers.fasta)
[2023-03-15 16:05:17,956] [INFO] Task started: Blastn
[2023-03-15 16:05:17,956] [INFO] Running command: blastn -query OceanDNA-b39298/markers.fasta -db /var/lib/cwl/stgbb09c4b8-9372-407f-a638-163ede536df6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b39298/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:05:19,042] [INFO] Task succeeded: Blastn
[2023-03-15 16:05:19,044] [INFO] Selected 32 target genomes.
[2023-03-15 16:05:19,044] [INFO] Target genome list was writen to OceanDNA-b39298/target_genomes_gtdb.txt
[2023-03-15 16:05:19,087] [INFO] Task started: fastANI
[2023-03-15 16:05:19,088] [INFO] Running command: fastANI --query /var/lib/cwl/stg9cf3637b-4736-4336-a10d-c5dc000d5785/OceanDNA-b39298.fa --refList OceanDNA-b39298/target_genomes_gtdb.txt --output OceanDNA-b39298/fastani_result_gtdb.tsv --threads 1
[2023-03-15 16:05:38,731] [INFO] Task succeeded: fastANI
[2023-03-15 16:05:38,747] [INFO] Found 27 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 16:05:38,747] [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_000961645.1	s__BRH-c0 sp000961645	79.2672	525	1120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__BRH-c0	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002702725.1	s__BRH-c0 sp002702725	78.5457	281	1120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__BRH-c0	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002388905.1	s__BRH-c0 sp002388905	77.4614	295	1120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__BRH-c0	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004801855.1	s__Pseudomonas_K sp004801855	77.0378	180	1120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	98.38	98.38	0.89	0.89	2	-
GCF_017255185.1	s__Parahaliea mediterranea_A	77.0272	211	1120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008064665.1	s__Parahaliea maris	76.8897	167	1120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003235325.1	s__SZUA-272 sp003235325	76.8849	144	1120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__SZUA-272	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003402235.1	s__Parahaliea mediterranea	76.8384	183	1120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001577635.1	s__Halomonas_C sp001577635	76.8286	131	1120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003182195.1	s__Halomonas sp003182195	76.8174	180	1120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.47	95.24	0.85	0.84	3	-
GCA_016708925.1	s__JAGPUQ01 sp016708925	76.7723	142	1120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__JAGPUQ01	95.0	98.16	98.04	0.89	0.89	3	-
GCA_016191205.1	s__JAGPUQ01 sp016191205	76.7102	141	1120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__JAGPUQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254665.1	s__Halomonas lactosivorans	76.6196	145	1120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003205495.1	s__Pseudomonas_E alcaligenes_B	76.5952	185	1120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187975.1	s__Pseudomonas delhiensis	76.5662	223	1120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.078	98.79	97.59	0.94	0.89	3	-
GCF_004327355.1	s__Pseudomonas_E dryadis	76.5601	159	1120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.58	99.16	0.96	0.92	3	-
GCF_009857815.1	s__Pseudomaricurvus sp009857815	76.4569	138	1120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Pseudomaricurvus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002341315.1	s__Porticoccus sp002341315	76.4535	61	1120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__Porticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101755.1	s__Pseudomonas_E alcaliphila	76.2737	129	1120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.74	97.49	0.95	0.92	3	-
GCF_000818015.1	s__Pseudomonas_A balearica	76.2607	126	1120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.54	98.20	0.91	0.86	18	-
GCF_004327335.1	s__Pseudomonas_Q kirkiae	76.2495	125	1120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_Q	95.0	99.65	99.41	0.96	0.94	4	-
GCF_004364315.1	s__Chromohalobacter marismortui	76.2439	52	1120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Chromohalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003935375.1	s__Pseudomonas_A xanthomarina_A	76.1782	105	1120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	97.0614	97.25	97.14	0.91	0.88	14	-
GCF_900110655.1	s__Pseudomonas_E soli	76.1462	121	1120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.13	95.09	0.90	0.88	23	-
GCF_019139675.1	s__Pseudomonas_E sp019139675	76.0974	132	1120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017912535.1	s__Motiliproteus sediminis	75.5233	59	1120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Motiliproteus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018069465.1	s__50-400-T64 sp018069465	75.4137	52	1120	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__50-400-T64	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-03-15 16:05:38,748] [INFO] GTDB search result was written to OceanDNA-b39298/result_gtdb.tsv
[2023-03-15 16:05:38,748] [INFO] ===== GTDB Search completed =====
[2023-03-15 16:05:38,753] [INFO] DFAST_QC result json was written to OceanDNA-b39298/dqc_result.json
[2023-03-15 16:05:38,753] [INFO] DFAST_QC completed!
[2023-03-15 16:05:38,753] [INFO] Total running time: 0h2m4s