[2023-03-17 22:46:02,579] [INFO] DFAST_QC pipeline started.
[2023-03-17 22:46:02,579] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 22:46:02,579] [INFO] DQC Reference Directory: /var/lib/cwl/stg23feeaca-fb52-432a-93e6-77174de0c589/dqc_reference
[2023-03-17 22:46:03,671] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 22:46:03,672] [INFO] Task started: Prodigal
[2023-03-17 22:46:03,672] [INFO] Running command: cat /var/lib/cwl/stgcb1debfb-3763-4d50-af11-8aff38b24c32/OceanDNA-b41232.fa | prodigal -d OceanDNA-b41232/cds.fna -a OceanDNA-b41232/protein.faa -g 11 -q > /dev/null
[2023-03-17 22:46:33,711] [INFO] Task succeeded: Prodigal
[2023-03-17 22:46:33,711] [INFO] Task started: HMMsearch
[2023-03-17 22:46:33,711] [INFO] Running command: hmmsearch --tblout OceanDNA-b41232/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg23feeaca-fb52-432a-93e6-77174de0c589/dqc_reference/reference_markers.hmm OceanDNA-b41232/protein.faa > /dev/null
[2023-03-17 22:46:34,115] [INFO] Task succeeded: HMMsearch
[2023-03-17 22:46:34,115] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgcb1debfb-3763-4d50-af11-8aff38b24c32/OceanDNA-b41232.fa]
[2023-03-17 22:46:34,143] [INFO] Query marker FASTA was written to OceanDNA-b41232/markers.fasta
[2023-03-17 22:46:34,144] [INFO] Task started: Blastn
[2023-03-17 22:46:34,144] [INFO] Running command: blastn -query OceanDNA-b41232/markers.fasta -db /var/lib/cwl/stg23feeaca-fb52-432a-93e6-77174de0c589/dqc_reference/reference_markers.fasta -out OceanDNA-b41232/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 22:46:37,908] [INFO] Task succeeded: Blastn
[2023-03-17 22:46:37,909] [INFO] Selected 13 target genomes.
[2023-03-17 22:46:37,909] [INFO] Target genome list was writen to OceanDNA-b41232/target_genomes.txt
[2023-03-17 22:46:37,918] [INFO] Task started: fastANI
[2023-03-17 22:46:37,918] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb1debfb-3763-4d50-af11-8aff38b24c32/OceanDNA-b41232.fa --refList OceanDNA-b41232/target_genomes.txt --output OceanDNA-b41232/fastani_result.tsv --threads 1
[2023-03-17 22:46:52,721] [INFO] Task succeeded: fastANI
[2023-03-17 22:46:52,721] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg23feeaca-fb52-432a-93e6-77174de0c589/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 22:46:52,721] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg23feeaca-fb52-432a-93e6-77174de0c589/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 22:46:52,730] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 22:46:52,730] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 22:46:52,730] [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 guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	87.092	1146	1568	95	below_threshold
Pseudomonas mendocina	strain=NBRC 14162	GCA_000813265.1	300	300	suspected-type	True	86.8116	1160	1568	95	below_threshold
Pseudomonas mendocina	strain=NCTC10897	GCA_900636545.1	300	300	suspected-type	True	86.7806	1180	1568	95	below_threshold
Pseudomonas yangonensis	strain=MY50	GCA_009932725.1	2579922	2579922	type	True	86.5691	1109	1568	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	86.5578	1104	1568	95	below_threshold
Pseudomonas sihuiensis	strain=KCTC 32246	GCA_900106015.1	1274359	1274359	type	True	86.538	1153	1568	95	below_threshold
Pseudomonas chengduensis	strain=MBR	GCA_017905455.1	489632	489632	type	True	86.4928	1141	1568	95	below_threshold
Pseudomonas toyotomiensis	strain=JCM 15604	GCA_900115695.1	554344	554344	type	True	86.4016	1154	1568	95	below_threshold
Pseudomonas toyotomiensis	strain=DSM 26169	GCA_002741095.1	554344	554344	type	True	86.378	1170	1568	95	below_threshold
Pseudomonas alcaligenes	strain=NCTC10367	GCA_900455475.1	43263	43263	type	True	82.8813	851	1568	95	below_threshold
Pseudomonas alcaligenes	strain=NBRC 14159	GCA_000467105.1	43263	43263	type	True	82.8534	859	1568	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	82.822	848	1568	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	81.7846	808	1568	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 22:46:52,730] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41232/tc_result.tsv
[2023-03-17 22:46:52,730] [INFO] ===== Taxonomy check completed =====
[2023-03-17 22:46:52,730] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 22:46:52,730] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg23feeaca-fb52-432a-93e6-77174de0c589/dqc_reference/checkm_data
[2023-03-17 22:46:52,731] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 22:46:52,737] [INFO] Task started: CheckM
[2023-03-17 22:46:52,737] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41232/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41232/checkm_input OceanDNA-b41232/checkm_result
[2023-03-17 22:48:04,390] [INFO] Task succeeded: CheckM
[2023-03-17 22:48:04,391] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.25%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 22:48:04,396] [INFO] ===== Completeness check finished =====
[2023-03-17 22:48:04,396] [INFO] ===== Start GTDB Search =====
[2023-03-17 22:48:04,396] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41232/markers.fasta)
[2023-03-17 22:48:04,397] [INFO] Task started: Blastn
[2023-03-17 22:48:04,397] [INFO] Running command: blastn -query OceanDNA-b41232/markers.fasta -db /var/lib/cwl/stg23feeaca-fb52-432a-93e6-77174de0c589/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41232/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 22:48:05,794] [INFO] Task succeeded: Blastn
[2023-03-17 22:48:05,795] [INFO] Selected 15 target genomes.
[2023-03-17 22:48:05,795] [INFO] Target genome list was writen to OceanDNA-b41232/target_genomes_gtdb.txt
[2023-03-17 22:48:05,811] [INFO] Task started: fastANI
[2023-03-17 22:48:05,811] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb1debfb-3763-4d50-af11-8aff38b24c32/OceanDNA-b41232.fa --refList OceanDNA-b41232/target_genomes_gtdb.txt --output OceanDNA-b41232/fastani_result_gtdb.tsv --threads 1
[2023-03-17 22:48:23,443] [INFO] Task succeeded: fastANI
[2023-03-17 22:48:23,452] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 22:48:23,452] [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_902506535.1	s__Pseudomonas_E sp902506535	88.0551	1131	1568	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_900104265.1	s__Pseudomonas_E guguanensis	87.1121	1144	1568	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.13	97.13	0.85	0.85	2	-
GCF_001567565.1	s__Pseudomonas_E composti_A	86.9959	1201	1568	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_000418555.1	s__Pseudomonas_E sp000418555	86.9086	1180	1568	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_900636545.1	s__Pseudomonas_E mendocina	86.7782	1181	1568	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.91	97.19	0.93	0.89	14	-
GCF_009932725.1	s__Pseudomonas_E sp009932725	86.5918	1106	1568	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.40	98.35	0.94	0.88	4	-
GCF_007049795.1	s__Pseudomonas_E mendocina_D	86.5636	1068	1568	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.17	96.47	0.87	0.84	6	-
GCF_002803095.1	s__Pseudomonas_E sp002803095	86.4699	1140	1568	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.6432	99.96	99.96	0.99	0.99	2	-
GCF_000016565.1	s__Pseudomonas_E mendocina_A	86.4203	1122	1568	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.76	97.37	0.90	0.88	7	-
GCF_900115695.1	s__Pseudomonas_E toyotomiensis	86.41	1153	1568	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.1942	98.17	97.23	0.91	0.85	7	-
GCF_004521985.1	s__Pseudomonas_E khazarica	86.3845	1183	1568	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.35	98.01	0.91	0.87	12	-
GCF_003696305.1	s__Pseudomonas_E sp003696305	86.0092	1049	1568	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_003205495.1	s__Pseudomonas_E alcaligenes_B	83.0996	847	1568	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_005508865.1	s__Pseudomonas_E sp005508865	82.8124	862	1568	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_000761545.1	s__Pseudomonas_E sp000761545	82.5652	875	1568	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 22:48:23,453] [INFO] GTDB search result was written to OceanDNA-b41232/result_gtdb.tsv
[2023-03-17 22:48:23,453] [INFO] ===== GTDB Search completed =====
[2023-03-17 22:48:23,455] [INFO] DFAST_QC result json was written to OceanDNA-b41232/dqc_result.json
[2023-03-17 22:48:23,455] [INFO] DFAST_QC completed!
[2023-03-17 22:48:23,455] [INFO] Total running time: 0h2m21s