[2023-03-17 07:01:49,598] [INFO] DFAST_QC pipeline started.
[2023-03-17 07:01:49,598] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 07:01:49,598] [INFO] DQC Reference Directory: /var/lib/cwl/stg166bc807-6eae-4c3f-8be1-288f89038d4b/dqc_reference
[2023-03-17 07:01:51,531] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 07:01:51,531] [INFO] Task started: Prodigal
[2023-03-17 07:01:51,531] [INFO] Running command: cat /var/lib/cwl/stg095ca390-e5e4-401d-bca9-ed90ab57f205/OceanDNA-b41317.fa | prodigal -d OceanDNA-b41317/cds.fna -a OceanDNA-b41317/protein.faa -g 11 -q > /dev/null
[2023-03-17 07:02:30,203] [INFO] Task succeeded: Prodigal
[2023-03-17 07:02:30,203] [INFO] Task started: HMMsearch
[2023-03-17 07:02:30,203] [INFO] Running command: hmmsearch --tblout OceanDNA-b41317/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg166bc807-6eae-4c3f-8be1-288f89038d4b/dqc_reference/reference_markers.hmm OceanDNA-b41317/protein.faa > /dev/null
[2023-03-17 07:02:30,477] [INFO] Task succeeded: HMMsearch
[2023-03-17 07:02:30,478] [INFO] Found 6/6 markers.
[2023-03-17 07:02:30,512] [INFO] Query marker FASTA was written to OceanDNA-b41317/markers.fasta
[2023-03-17 07:02:30,513] [INFO] Task started: Blastn
[2023-03-17 07:02:30,513] [INFO] Running command: blastn -query OceanDNA-b41317/markers.fasta -db /var/lib/cwl/stg166bc807-6eae-4c3f-8be1-288f89038d4b/dqc_reference/reference_markers.fasta -out OceanDNA-b41317/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:02:31,329] [INFO] Task succeeded: Blastn
[2023-03-17 07:02:31,330] [INFO] Selected 25 target genomes.
[2023-03-17 07:02:31,331] [INFO] Target genome list was writen to OceanDNA-b41317/target_genomes.txt
[2023-03-17 07:02:31,345] [INFO] Task started: fastANI
[2023-03-17 07:02:31,346] [INFO] Running command: fastANI --query /var/lib/cwl/stg095ca390-e5e4-401d-bca9-ed90ab57f205/OceanDNA-b41317.fa --refList OceanDNA-b41317/target_genomes.txt --output OceanDNA-b41317/fastani_result.tsv --threads 1
[2023-03-17 07:03:01,152] [INFO] Task succeeded: fastANI
[2023-03-17 07:03:01,152] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg166bc807-6eae-4c3f-8be1-288f89038d4b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 07:03:01,153] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg166bc807-6eae-4c3f-8be1-288f89038d4b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 07:03:01,166] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 07:03:01,167] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 07:03:01,167] [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
Pseudomonas extremaustralis	strain=DSM 17835	GCA_900102035.1	359110	359110	type	True	89.7045	1448	1943	95	below_threshold
Pseudomonas extremaustralis		GCA_900625045.1	359110	359110	type	True	89.6982	1427	1943	95	below_threshold
Pseudomonas extremaustralis	strain=14-3 substr. 14-3b	GCA_000242115.2	359110	359110	type	True	89.6836	1421	1943	95	below_threshold
Pseudomonas extremaustralis	strain=DSM 17835	GCA_007858235.1	359110	359110	type	True	89.6617	1447	1943	95	below_threshold
Pseudomonas marginalis	strain=DSM 13124	GCA_007858155.1	298	298	suspected-type	True	89.0293	1493	1943	95	below_threshold
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	88.6246	1418	1943	95	below_threshold
Pseudomonas marginalis	strain=ICMP 3553	GCA_003700725.1	298	298	suspected-type	True	88.535	1373	1943	95	below_threshold
Pseudomonas marginalis	strain=ICMP 3553	GCA_001645105.1	298	298	suspected-type	True	88.5218	1447	1943	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	88.3759	1423	1943	95	below_threshold
Pseudomonas fluorescens	strain=NBRC 14160	GCA_002091595.1	294	294	suspected-type	True	88.1381	1429	1943	95	below_threshold
Pseudomonas salomonii	strain=ICMP 14252	GCA_900107155.1	191391	191391	type	True	88.0721	1432	1943	95	below_threshold
Pseudomonas salomonii	strain=LMG 22120	GCA_001730645.1	191391	191391	type	True	88.0423	1433	1943	95	below_threshold
Pseudomonas fluorescens	strain=DSM 50090	GCA_007858165.1	294	294	suspected-type	True	88.037	1456	1943	95	below_threshold
Pseudomonas fluorescens	strain=NCTC10038	GCA_900475215.1	294	294	suspected-type	True	88.0258	1458	1943	95	below_threshold
Pseudomonas paracarnis	strain=V5/DAB/2/5	GCA_904063055.1	2750625	2750625	type	True	87.7492	1369	1943	95	below_threshold
Pseudomonas yamanorum	strain=LMG 27247	GCA_900105735.1	515393	515393	suspected-type	True	87.1695	1412	1943	95	below_threshold
Pseudomonas proteolytica	strain=DSM 15321	GCA_007858275.1	219574	219574	type	True	86.6085	1265	1943	95	below_threshold
Pseudomonas spelaei	strain=CCM 7893	GCA_009724245.1	1055469	1055469	type	True	86.2287	1357	1943	95	below_threshold
Pseudomonas karstica	strain=CCM 7891	GCA_009707515.1	1055468	1055468	type	True	85.5084	1205	1943	95	below_threshold
Halomonas pantelleriensis	strain=AAP	GCA_900102875.1	48727	48727	type	True	76.4851	178	1943	95	below_threshold
Halomonas ventosae	strain=CECT 5797	GCA_004363555.1	229007	229007	type	True	76.2672	187	1943	95	below_threshold
Halomonas shengliensis	strain=CGMCC 1.6444	GCA_900104135.1	419597	419597	type	True	76.2414	199	1943	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	75.9415	143	1943	95	below_threshold
Halomonas icarae	strain=D1-1	GCA_009901955.1	2691040	2691040	type	True	75.9149	123	1943	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 07:03:01,167] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41317/tc_result.tsv
[2023-03-17 07:03:01,167] [INFO] ===== Taxonomy check completed =====
[2023-03-17 07:03:01,167] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 07:03:01,167] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg166bc807-6eae-4c3f-8be1-288f89038d4b/dqc_reference/checkm_data
[2023-03-17 07:03:01,168] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 07:03:01,182] [INFO] Task started: CheckM
[2023-03-17 07:03:01,182] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41317/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41317/checkm_input OceanDNA-b41317/checkm_result
[2023-03-17 07:04:33,630] [INFO] Task succeeded: CheckM
[2023-03-17 07:04:33,631] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 07:04:33,661] [INFO] ===== Completeness check finished =====
[2023-03-17 07:04:33,661] [INFO] ===== Start GTDB Search =====
[2023-03-17 07:04:33,662] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41317/markers.fasta)
[2023-03-17 07:04:33,662] [INFO] Task started: Blastn
[2023-03-17 07:04:33,662] [INFO] Running command: blastn -query OceanDNA-b41317/markers.fasta -db /var/lib/cwl/stg166bc807-6eae-4c3f-8be1-288f89038d4b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41317/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:04:35,005] [INFO] Task succeeded: Blastn
[2023-03-17 07:04:35,006] [INFO] Selected 31 target genomes.
[2023-03-17 07:04:35,006] [INFO] Target genome list was writen to OceanDNA-b41317/target_genomes_gtdb.txt
[2023-03-17 07:04:35,153] [INFO] Task started: fastANI
[2023-03-17 07:04:35,153] [INFO] Running command: fastANI --query /var/lib/cwl/stg095ca390-e5e4-401d-bca9-ed90ab57f205/OceanDNA-b41317.fa --refList OceanDNA-b41317/target_genomes_gtdb.txt --output OceanDNA-b41317/fastani_result_gtdb.tsv --threads 1
[2023-03-17 07:05:19,189] [INFO] Task succeeded: fastANI
[2023-03-17 07:05:19,206] [INFO] Found 31 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 07:05:19,206] [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_001439695.1	s__Pseudomonas_E veronii	98.7879	1773	1943	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.79	98.13	0.89	0.82	43	conclusive
GCF_900102035.1	s__Pseudomonas_E extremaustralis	89.6983	1449	1943	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.74	98.99	0.98	0.92	5	-
GCF_001050345.1	s__Pseudomonas_E fildesensis	89.3653	1484	1943	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_001708445.1	s__Pseudomonas_E fluorescens_AN	89.234	1565	1943	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.17	98.56	0.90	0.82	34	-
GCF_014207255.1	s__Pseudomonas_E sp014207255	89.0703	1510	1943	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.31	98.90	0.95	0.91	5	-
GCF_900105325.1	s__Pseudomonas_E marginalis	89.0156	1515	1943	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.53	96.47	0.90	0.85	19	-
GCF_003097075.1	s__Pseudomonas_E sp003097075	88.9171	1426	1943	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.77	98.77	0.94	0.94	2	-
GCF_900580675.1	s__Pseudomonas_E sp900580675	88.7972	1346	1943	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_002843605.1	s__Pseudomonas_E sp002843605	88.7189	1459	1943	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.70	97.45	0.92	0.91	7	-
GCF_900591205.1	s__Pseudomonas_E sp900591205	88.6422	1451	1943	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_001645105.1	s__Pseudomonas_E marginalis_B	88.5159	1448	1943	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.70	98.28	0.91	0.87	10	-
GCF_009834565.1	s__Pseudomonas_E sp009834565	88.5069	1459	1943	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.71	97.35	0.93	0.93	3	-
GCF_002563895.1	s__Pseudomonas_E lurida	88.3884	1421	1943	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.19	99.03	0.94	0.91	25	-
GCF_009866765.1	s__Pseudomonas_E sp009866765	88.3814	1439	1943	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_014851685.1	s__Pseudomonas_E sp014851685	88.3503	1434	1943	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_001186335.1	s__Pseudomonas_E trivialis_B	88.3147	1447	1943	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.34	95.31	0.86	0.86	8	-
GCF_001647715.1	s__Pseudomonas_E antarctica_A	88.2005	1424	1943	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.45	97.45	0.91	0.91	2	-
GCF_003852315.1	s__Pseudomonas_E sp003014915	88.1696	1431	1943	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.48	96.20	0.95	0.91	10	-
GCF_004682045.1	s__Pseudomonas_E nabeulensis	88.1034	1353	1943	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.61	95.59	0.85	0.85	3	-
GCF_900107155.1	s__Pseudomonas_E salomonii	88.0879	1430	1943	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.30	96.43	0.92	0.87	14	-
GCF_001983175.1	s__Pseudomonas_E cedrina	88.0167	1412	1943	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.10	97.30	0.97	0.92	4	-
GCF_003851685.1	s__Pseudomonas_E sp003851685	87.8002	1385	1943	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_002837185.1	s__Pseudomonas_E fluorescens_AM	87.7893	1349	1943	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.23	99.16	0.96	0.94	7	-
GCF_904063055.1	s__Pseudomonas_E paracarnis	87.7434	1370	1943	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.75	95.59	0.90	0.84	86	-
GCF_000263715.2	s__Pseudomonas_E synxantha_A	87.5899	1378	1943	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.66	97.33	0.90	0.88	8	-
GCF_002874965.1	s__Pseudomonas_E sp002874965	87.4384	1413	1943	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.77	98.46	0.92	0.88	48	-
GCF_013386825.1	s__Pseudomonas_E sp013386825	87.316	1356	1943	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.99	99.99	0.99	0.99	2	-
GCF_002204795.1	s__Pseudomonas_E sp002204795	87.2495	1413	1943	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_001952855.1	s__Pseudomonas_E sp001952855	87.1883	1387	1943	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.78	98.78	0.94	0.94	2	-
GCF_013403585.1	s__Pseudomonas_E yamanorum_B	86.1944	1359	1943	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.31	98.31	0.89	0.89	2	-
GCF_018614775.1	s__Pseudomonas_E fluorescens_BY	83.6698	1036	1943	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 07:05:19,206] [INFO] GTDB search result was written to OceanDNA-b41317/result_gtdb.tsv
[2023-03-17 07:05:19,206] [INFO] ===== GTDB Search completed =====
[2023-03-17 07:05:19,209] [INFO] DFAST_QC result json was written to OceanDNA-b41317/dqc_result.json
[2023-03-17 07:05:19,209] [INFO] DFAST_QC completed!
[2023-03-17 07:05:19,209] [INFO] Total running time: 0h3m30s