[2023-03-17 15:54:38,100] [INFO] DFAST_QC pipeline started.
[2023-03-17 15:54:38,101] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 15:54:38,101] [INFO] DQC Reference Directory: /var/lib/cwl/stgba87719e-67fa-4d08-8cb1-31580f9cc1dd/dqc_reference
[2023-03-17 15:54:39,319] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 15:54:39,320] [INFO] Task started: Prodigal
[2023-03-17 15:54:39,320] [INFO] Running command: cat /var/lib/cwl/stg18778d3e-fd7d-4774-80df-45cb4eaa8274/OceanDNA-b20958.fa | prodigal -d OceanDNA-b20958/cds.fna -a OceanDNA-b20958/protein.faa -g 11 -q > /dev/null
[2023-03-17 15:55:15,028] [INFO] Task succeeded: Prodigal
[2023-03-17 15:55:15,028] [INFO] Task started: HMMsearch
[2023-03-17 15:55:15,028] [INFO] Running command: hmmsearch --tblout OceanDNA-b20958/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgba87719e-67fa-4d08-8cb1-31580f9cc1dd/dqc_reference/reference_markers.hmm OceanDNA-b20958/protein.faa > /dev/null
[2023-03-17 15:55:15,312] [INFO] Task succeeded: HMMsearch
[2023-03-17 15:55:15,313] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg18778d3e-fd7d-4774-80df-45cb4eaa8274/OceanDNA-b20958.fa]
[2023-03-17 15:55:15,360] [INFO] Query marker FASTA was written to OceanDNA-b20958/markers.fasta
[2023-03-17 15:55:15,360] [INFO] Task started: Blastn
[2023-03-17 15:55:15,360] [INFO] Running command: blastn -query OceanDNA-b20958/markers.fasta -db /var/lib/cwl/stgba87719e-67fa-4d08-8cb1-31580f9cc1dd/dqc_reference/reference_markers.fasta -out OceanDNA-b20958/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 15:55:16,012] [INFO] Task succeeded: Blastn
[2023-03-17 15:55:16,013] [INFO] Selected 39 target genomes.
[2023-03-17 15:55:16,014] [INFO] Target genome list was writen to OceanDNA-b20958/target_genomes.txt
[2023-03-17 15:55:16,100] [INFO] Task started: fastANI
[2023-03-17 15:55:16,100] [INFO] Running command: fastANI --query /var/lib/cwl/stg18778d3e-fd7d-4774-80df-45cb4eaa8274/OceanDNA-b20958.fa --refList OceanDNA-b20958/target_genomes.txt --output OceanDNA-b20958/fastani_result.tsv --threads 1
[2023-03-17 15:55:47,533] [INFO] Task succeeded: fastANI
[2023-03-17 15:55:47,533] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgba87719e-67fa-4d08-8cb1-31580f9cc1dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 15:55:47,533] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgba87719e-67fa-4d08-8cb1-31580f9cc1dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 15:55:47,550] [INFO] Found 33 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 15:55:47,550] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 15:55:47,551] [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
Luteimonas aestuarii	strain=B9	GCA_004357985.1	453837	453837	type	True	75.1511	84	1931	95	below_threshold
Pseudoxanthomonas japonensis	strain=DSM 17109	GCA_010093445.1	69284	69284	type	True	75.1268	106	1931	95	below_threshold
Pseudoxanthomonas taiwanensis	strain=DSM 22914	GCA_010093135.1	176598	176598	type	True	75.0255	147	1931	95	below_threshold
Corallococcus soli	strain=ZKHCc1 1396	GCA_014930455.1	2710757	2710757	type	True	74.9371	208	1931	95	below_threshold
Blastochloris tepida	strain=GI	GCA_003966715.1	2233851	2233851	type	True	74.9253	127	1931	95	below_threshold
Xanthomonas massiliensis	strain=SN8	GCA_900018785.1	1720302	1720302	type	True	74.9172	131	1931	95	below_threshold
Alcanivorax marinus	strain=R8-12	GCA_025532125.1	1177169	1177169	type	True	74.8938	76	1931	95	below_threshold
Corallococcus llansteffanensis	strain=CA051B	GCA_003612055.1	2316731	2316731	type	True	74.8937	205	1931	95	below_threshold
Methylobacterium jeotgali	strain=LMG 23639	GCA_022179345.1	381630	381630	type	True	74.8727	170	1931	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	74.861	320	1931	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	74.849	169	1931	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	74.8488	311	1931	95	below_threshold
Thiorhodococcus mannitoliphagus	strain=DSM 18266	GCA_010915725.1	329406	329406	type	True	74.8464	65	1931	95	below_threshold
Ornithinimicrobium sediminis	strain=EGI L100131	GCA_021272345.1	2904603	2904603	type	True	74.8452	120	1931	95	below_threshold
Corallococcus terminator	strain=CA054A	GCA_003611635.1	2316733	2316733	type	True	74.8276	192	1931	95	below_threshold
Corallococcus praedator	strain=CA031B	GCA_003612125.1	2316724	2316724	type	True	74.8205	192	1931	95	below_threshold
Nocardia shimofusensis	strain=NBRC 100134	GCA_001613125.1	228596	228596	type	True	74.8199	148	1931	95	below_threshold
Corallococcus sicarius	strain=CA040B	GCA_003611735.1	2316726	2316726	type	True	74.8178	196	1931	95	below_threshold
Crenobacter intestini	strain=GY 70310	GCA_004919095.1	2563443	2563443	type	True	74.8159	91	1931	95	below_threshold
Ideonella livida	strain=TBM-1	GCA_010499455.1	2707176	2707176	type	True	74.8055	148	1931	95	below_threshold
Nocardia higoensis	strain=NBRC 100133	GCA_000308595.1	228599	228599	type	True	74.7964	178	1931	95	below_threshold
Rhizobacter gummiphilus	strain=NS21	GCA_002116905.1	946333	946333	type	True	74.7957	160	1931	95	below_threshold
Rhizobacter gummiphilus	strain=NBRC 109400	GCA_002762215.1	946333	946333	type	True	74.794	161	1931	95	below_threshold
Massilia alkalitolerans	strain=DSM 17462	GCA_000427785.1	286638	286638	type	True	74.7881	140	1931	95	below_threshold
Albimonas pacifica	strain=CGMCC 1.11030	GCA_900113695.1	1114924	1114924	type	True	74.7838	251	1931	95	below_threshold
Methylobacterium aerolatum	strain=DSM 19013	GCA_022179085.1	418708	418708	type	True	74.7756	135	1931	95	below_threshold
Dokdonella koreensis	strain=DS-123	GCA_001632775.1	323415	323415	type	True	74.7487	162	1931	95	below_threshold
Sphaerisporangium rufum	strain=NBRC 109079	GCA_016863395.1	1381558	1381558	type	True	74.7474	273	1931	95	below_threshold
Massilia oculi	strain=CCUG 43427	GCA_003143515.1	945844	945844	type	True	74.7122	126	1931	95	below_threshold
Massilia yuzhufengensis	strain=CGMCC 1.12041	GCA_900112225.1	1164594	1164594	type	True	74.6823	110	1931	95	below_threshold
Massilia cavernae	strain=K1S02-61	GCA_003590855.1	2320864	2320864	type	True	74.675	77	1931	95	below_threshold
Halosimplex halophilum	strain=TH32	GCA_004698125.1	2559572	2559572	type	True	74.641	147	1931	95	below_threshold
Massilia aromaticivorans	strain=ML15P13	GCA_013003915.1	2725995	2725995	type	True	74.6208	97	1931	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 15:55:47,551] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20958/tc_result.tsv
[2023-03-17 15:55:47,551] [INFO] ===== Taxonomy check completed =====
[2023-03-17 15:55:47,551] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 15:55:47,551] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgba87719e-67fa-4d08-8cb1-31580f9cc1dd/dqc_reference/checkm_data
[2023-03-17 15:55:47,552] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 15:55:47,560] [INFO] Task started: CheckM
[2023-03-17 15:55:47,560] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20958/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20958/checkm_input OceanDNA-b20958/checkm_result
[2023-03-17 15:57:33,379] [INFO] Task succeeded: CheckM
[2023-03-17 15:57:33,379] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 15:57:33,384] [INFO] ===== Completeness check finished =====
[2023-03-17 15:57:33,384] [INFO] ===== Start GTDB Search =====
[2023-03-17 15:57:33,384] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20958/markers.fasta)
[2023-03-17 15:57:33,387] [INFO] Task started: Blastn
[2023-03-17 15:57:33,387] [INFO] Running command: blastn -query OceanDNA-b20958/markers.fasta -db /var/lib/cwl/stgba87719e-67fa-4d08-8cb1-31580f9cc1dd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20958/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 15:57:34,495] [INFO] Task succeeded: Blastn
[2023-03-17 15:57:34,496] [INFO] Selected 27 target genomes.
[2023-03-17 15:57:34,496] [INFO] Target genome list was writen to OceanDNA-b20958/target_genomes_gtdb.txt
[2023-03-17 15:57:34,955] [INFO] Task started: fastANI
[2023-03-17 15:57:34,955] [INFO] Running command: fastANI --query /var/lib/cwl/stg18778d3e-fd7d-4774-80df-45cb4eaa8274/OceanDNA-b20958.fa --refList OceanDNA-b20958/target_genomes_gtdb.txt --output OceanDNA-b20958/fastani_result_gtdb.tsv --threads 1
[2023-03-17 15:58:01,068] [INFO] Task succeeded: fastANI
[2023-03-17 15:58:01,081] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 15:58:01,082] [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_007693595.1	s__REDI01 sp007693595	76.7898	303	1931	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__GCA-2862545;g__REDI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006226595.1	s__M1803 sp006226595	76.2905	410	1931	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__GCA-2862545;g__M1803	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862545.1	s__GCA-2862545 sp002862545	75.978	208	1931	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__GCA-2862545;g__GCA-2862545	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011376105.1	s__DRPG01 sp011376105	75.7854	226	1931	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__GCA-2862545;g__DRPG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903861005.1	s__CAIOSP01 sp903861005	75.72	269	1931	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__GCA-2862545;g__CAIOSP01	95.0	99.96	99.95	0.97	0.97	4	-
GCA_903959175.1	s__CAJBVW01 sp903959175	75.5427	330	1931	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__CAJBVW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903921785.1	s__SXON01 sp903921785	75.4393	292	1931	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__SXON01	95.0	99.91	99.91	0.96	0.95	4	-
GCA_016938035.1	s__JAFGVK01 sp016938035	75.4216	209	1931	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__GCA-2862545;g__JAFGVK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016717595.1	s__JADKFE01 sp016717595	75.3523	273	1931	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__CAJQPC01;g__JADKFE01	95.0	98.32	98.16	0.91	0.88	3	-
GCA_903885375.1	s__SXON01 sp903885375	75.3162	232	1931	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__SXON01	95.0	99.91	99.89	0.96	0.95	10	-
GCF_000964525.1	s__Anaeromyxobacter sp000964525	75.1629	204	1931	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__Anaeromyxobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011064545.1	s__XN24 sp011064545	75.1109	59	1931	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__XN24;f__XN24;g__XN24	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240295.1	s__Plasticicumulans sp003962905	74.9553	163	1931	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Plasticicumulans	95.0	98.50	98.50	0.84	0.84	2	-
GCA_001899075.1	s__Devosia_A sp001899075	74.9268	100	1931	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	100.00	100.00	0.99	0.99	2	-
GCF_011089885.1	s__XN24 sp011089885	74.9216	79	1931	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__XN24;f__XN24;g__XN24	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002863005.1	s__Pseudoxanthomonas_A sp002863005	74.913	91	1931	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109915.1	s__Luteibacter sp900109915	74.9084	83	1931	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650495.1	s__Streptomyces cinnamoneus	74.853	220	1931	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015277795.1	s__Massilia sp015277795	74.7436	116	1931	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745265.1	s__Massilia sp000745265	74.7416	128	1931	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003223165.1	s__QHXZ01 sp003223165	74.7035	88	1931	d__Bacteria;p__Acidobacteriota;c__Mor1;o__Gp22-AA2;f__Gp22-AA2;g__QHXZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003177035.1	s__Salinisphaera sp003177035	74.6989	52	1931	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003590855.1	s__Massilia sp003590855	74.674	78	1931	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002450985.1	s__UBA6912 sp002450985	74.6011	89	1931	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__UBA5794;f__UBA5794;g__UBA6912	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 15:58:01,082] [INFO] GTDB search result was written to OceanDNA-b20958/result_gtdb.tsv
[2023-03-17 15:58:01,082] [INFO] ===== GTDB Search completed =====
[2023-03-17 15:58:01,085] [INFO] DFAST_QC result json was written to OceanDNA-b20958/dqc_result.json
[2023-03-17 15:58:01,085] [INFO] DFAST_QC completed!
[2023-03-17 15:58:01,085] [INFO] Total running time: 0h3m23s