[2023-03-17 22:37:11,859] [INFO] DFAST_QC pipeline started.
[2023-03-17 22:37:11,859] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 22:37:11,859] [INFO] DQC Reference Directory: /var/lib/cwl/stgc6d2d449-c1a9-4ebe-be1e-4bb9e7eee7fe/dqc_reference
[2023-03-17 22:37:12,985] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 22:37:12,986] [INFO] Task started: Prodigal
[2023-03-17 22:37:12,986] [INFO] Running command: cat /var/lib/cwl/stg65a887ea-8e69-45cf-b4e8-180f93c1d7c0/OceanDNA-b41235.fa | prodigal -d OceanDNA-b41235/cds.fna -a OceanDNA-b41235/protein.faa -g 11 -q > /dev/null
[2023-03-17 22:37:45,604] [INFO] Task succeeded: Prodigal
[2023-03-17 22:37:45,604] [INFO] Task started: HMMsearch
[2023-03-17 22:37:45,604] [INFO] Running command: hmmsearch --tblout OceanDNA-b41235/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc6d2d449-c1a9-4ebe-be1e-4bb9e7eee7fe/dqc_reference/reference_markers.hmm OceanDNA-b41235/protein.faa > /dev/null
[2023-03-17 22:37:45,843] [INFO] Task succeeded: HMMsearch
[2023-03-17 22:37:45,844] [INFO] Found 6/6 markers.
[2023-03-17 22:37:45,870] [INFO] Query marker FASTA was written to OceanDNA-b41235/markers.fasta
[2023-03-17 22:37:45,871] [INFO] Task started: Blastn
[2023-03-17 22:37:45,871] [INFO] Running command: blastn -query OceanDNA-b41235/markers.fasta -db /var/lib/cwl/stgc6d2d449-c1a9-4ebe-be1e-4bb9e7eee7fe/dqc_reference/reference_markers.fasta -out OceanDNA-b41235/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 22:37:46,831] [INFO] Task succeeded: Blastn
[2023-03-17 22:37:46,832] [INFO] Selected 17 target genomes.
[2023-03-17 22:37:46,832] [INFO] Target genome list was writen to OceanDNA-b41235/target_genomes.txt
[2023-03-17 22:37:46,839] [INFO] Task started: fastANI
[2023-03-17 22:37:46,839] [INFO] Running command: fastANI --query /var/lib/cwl/stg65a887ea-8e69-45cf-b4e8-180f93c1d7c0/OceanDNA-b41235.fa --refList OceanDNA-b41235/target_genomes.txt --output OceanDNA-b41235/fastani_result.tsv --threads 1
[2023-03-17 22:38:06,949] [INFO] Task succeeded: fastANI
[2023-03-17 22:38:06,949] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc6d2d449-c1a9-4ebe-be1e-4bb9e7eee7fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 22:38:06,949] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc6d2d449-c1a9-4ebe-be1e-4bb9e7eee7fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 22:38:06,959] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 22:38:06,959] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 22:38:06,959] [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 faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	86.7589	1254	1685	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	86.6923	1193	1685	95	below_threshold
Pseudomonas plecoglossicida	strain=DSM 15088	GCA_000688275.1	70775	70775	suspected-type	True	86.3127	1205	1685	95	below_threshold
Pseudomonas plecoglossicida	strain=NBRC 103162	GCA_000730665.1	70775	70775	suspected-type	True	86.3091	1195	1685	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_021602465.1	2740517	2740517	suspected-type	True	86.1206	1245	1685	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_013373915.1	2740517	2740517	suspected-type	True	86.113	1215	1685	95	below_threshold
Pseudomonas anuradhapurensis	strain=RD8MR3	GCA_014269225.2	485870	485870	type	True	86.0143	1203	1685	95	below_threshold
Pseudomonas muyukensis	strain=COW39	GCA_019139535.1	2842357	2842357	type	True	85.8264	1198	1685	95	below_threshold
Pseudomonas xantholysinigenes	strain=RW9S1A	GCA_014268885.2	2745490	2745490	type	True	85.7817	1149	1685	95	below_threshold
Pseudomonas oryzicola	strain=RD9SR1	GCA_014269185.2	485876	485876	type	True	85.7592	1192	1685	95	below_threshold
Pseudomonas mosselii	strain=DSM 17497	GCA_019823065.1	78327	78327	type	True	85.5719	1204	1685	95	below_threshold
Pseudomonas putida	strain=IPO3752	GCA_013387005.1	303	303	suspected-type	True	85.5257	1236	1685	95	below_threshold
Pseudomonas monteilii	strain=NBRC 103158	GCA_000730605.1	76759	76759	type	True	85.4944	1211	1685	95	below_threshold
Pseudomonas monteilii	strain=DSM 14164	GCA_000621245.1	76759	76759	type	True	85.492	1233	1685	95	below_threshold
Pseudomonas kermanshahensis	strain=SWRI100	GCA_014269205.2	2745482	2745482	type	True	85.4847	1237	1685	95	below_threshold
Pseudomonas maumuensis	strain=COW77	GCA_019139675.1	2842354	2842354	type	True	85.4689	1172	1685	95	below_threshold
Pseudomonas ceruminis	strain=BML-PP028	GCA_013373895.1	2740516	2740516	type	True	85.3376	1192	1685	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 22:38:06,959] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41235/tc_result.tsv
[2023-03-17 22:38:06,959] [INFO] ===== Taxonomy check completed =====
[2023-03-17 22:38:06,960] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 22:38:06,960] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc6d2d449-c1a9-4ebe-be1e-4bb9e7eee7fe/dqc_reference/checkm_data
[2023-03-17 22:38:06,960] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 22:38:06,967] [INFO] Task started: CheckM
[2023-03-17 22:38:06,967] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41235/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41235/checkm_input OceanDNA-b41235/checkm_result
[2023-03-17 22:39:26,719] [INFO] Task succeeded: CheckM
[2023-03-17 22:39:26,720] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.52%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 22:39:26,723] [INFO] ===== Completeness check finished =====
[2023-03-17 22:39:26,723] [INFO] ===== Start GTDB Search =====
[2023-03-17 22:39:26,724] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41235/markers.fasta)
[2023-03-17 22:39:26,725] [INFO] Task started: Blastn
[2023-03-17 22:39:26,725] [INFO] Running command: blastn -query OceanDNA-b41235/markers.fasta -db /var/lib/cwl/stgc6d2d449-c1a9-4ebe-be1e-4bb9e7eee7fe/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41235/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 22:39:28,613] [INFO] Task succeeded: Blastn
[2023-03-17 22:39:28,614] [INFO] Selected 16 target genomes.
[2023-03-17 22:39:28,615] [INFO] Target genome list was writen to OceanDNA-b41235/target_genomes_gtdb.txt
[2023-03-17 22:39:28,799] [INFO] Task started: fastANI
[2023-03-17 22:39:28,799] [INFO] Running command: fastANI --query /var/lib/cwl/stg65a887ea-8e69-45cf-b4e8-180f93c1d7c0/OceanDNA-b41235.fa --refList OceanDNA-b41235/target_genomes_gtdb.txt --output OceanDNA-b41235/fastani_result_gtdb.tsv --threads 1
[2023-03-17 22:39:50,045] [INFO] Task succeeded: fastANI
[2023-03-17 22:39:50,055] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 22:39:50,055] [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_004357765.1	s__Pseudomonas_E putida_U	99.2788	1533	1685	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.43	99.43	0.90	0.90	2	conclusive
GCF_005080685.1	s__Pseudomonas_E putida_V	89.8763	1431	1685	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_016648105.1	s__Pseudomonas_E sp016648105	88.7918	1360	1685	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_002112505.1	s__Pseudomonas_E sp002112505	86.5546	1290	1685	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	0.99	6	-
GCF_000730665.1	s__Pseudomonas_E plecoglossicida	86.3109	1195	1685	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.81	99.74	0.97	0.95	6	-
GCF_003331055.1	s__Pseudomonas_E sp003331055	86.2627	1162	1685	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_000282535.1	s__Pseudomonas_E sp000282535	86.2197	1124	1685	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_001642705.1	s__Pseudomonas_E sp001642705	86.1884	1217	1685	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.26	95.01	0.89	0.85	3	-
GCF_000935045.1	s__Pseudomonas_E sp000935045	86.188	1227	1685	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_009932335.1	s__Pseudomonas_E asiatica	86.0482	1254	1685	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0481	97.98	96.05	0.89	0.79	58	-
GCA_003428805.1	s__Pseudomonas_E sp003428805	86.0347	1263	1685	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.29	96.05	0.90	0.83	9	-
GCF_015680405.1	s__Pseudomonas_E pudica	85.9478	1229	1685	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0481	98.52	95.23	0.90	0.83	12	-
GCF_019139535.1	s__Pseudomonas_E sp019139535	85.8171	1199	1685	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_011752525.1	s__Pseudomonas_E sp011752525	85.7002	1109	1685	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_004519305.1	s__Pseudomonas_E sp004519305	85.5563	1144	1685	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_014268975.1	s__Pseudomonas_E sp014268975	85.0519	1178	1685	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.16	99.15	0.95	0.95	3	-
--------------------------------------------------------------------------------
[2023-03-17 22:39:50,055] [INFO] GTDB search result was written to OceanDNA-b41235/result_gtdb.tsv
[2023-03-17 22:39:50,055] [INFO] ===== GTDB Search completed =====
[2023-03-17 22:39:50,057] [INFO] DFAST_QC result json was written to OceanDNA-b41235/dqc_result.json
[2023-03-17 22:39:50,057] [INFO] DFAST_QC completed!
[2023-03-17 22:39:50,057] [INFO] Total running time: 0h2m38s