[2023-03-15 11:51:17,349] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:51:17,349] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:51:17,349] [INFO] DQC Reference Directory: /var/lib/cwl/stg2a1c7fa0-4376-42dd-8bbd-10ff60d2adfc/dqc_reference
[2023-03-15 11:51:18,955] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:51:18,955] [INFO] Task started: Prodigal
[2023-03-15 11:51:18,956] [INFO] Running command: cat /var/lib/cwl/stg8f30cbe4-59b4-45e4-a562-443edd7f5125/OceanDNA-b41046.fa | prodigal -d OceanDNA-b41046/cds.fna -a OceanDNA-b41046/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:51:38,323] [INFO] Task succeeded: Prodigal
[2023-03-15 11:51:38,323] [INFO] Task started: HMMsearch
[2023-03-15 11:51:38,323] [INFO] Running command: hmmsearch --tblout OceanDNA-b41046/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2a1c7fa0-4376-42dd-8bbd-10ff60d2adfc/dqc_reference/reference_markers.hmm OceanDNA-b41046/protein.faa > /dev/null
[2023-03-15 11:51:38,536] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:51:38,536] [INFO] Found 6/6 markers.
[2023-03-15 11:51:38,557] [INFO] Query marker FASTA was written to OceanDNA-b41046/markers.fasta
[2023-03-15 11:51:38,557] [INFO] Task started: Blastn
[2023-03-15 11:51:38,557] [INFO] Running command: blastn -query OceanDNA-b41046/markers.fasta -db /var/lib/cwl/stg2a1c7fa0-4376-42dd-8bbd-10ff60d2adfc/dqc_reference/reference_markers.fasta -out OceanDNA-b41046/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:51:39,254] [INFO] Task succeeded: Blastn
[2023-03-15 11:51:39,255] [INFO] Selected 22 target genomes.
[2023-03-15 11:51:39,255] [INFO] Target genome list was writen to OceanDNA-b41046/target_genomes.txt
[2023-03-15 11:51:39,270] [INFO] Task started: fastANI
[2023-03-15 11:51:39,270] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f30cbe4-59b4-45e4-a562-443edd7f5125/OceanDNA-b41046.fa --refList OceanDNA-b41046/target_genomes.txt --output OceanDNA-b41046/fastani_result.tsv --threads 1
[2023-03-15 11:51:55,588] [INFO] Task succeeded: fastANI
[2023-03-15 11:51:55,588] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2a1c7fa0-4376-42dd-8bbd-10ff60d2adfc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:51:55,589] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2a1c7fa0-4376-42dd-8bbd-10ff60d2adfc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:51:55,601] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:51:55,602] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 11:51:55,602] [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
Halopseudomonas salina	strain=CGMCC 1.12482	GCA_014637955.1	1323744	1323744	type	True	80.2184	556	1048	95	below_threshold
Halopseudomonas salina	strain=XCD-X85	GCA_008641105.1	1323744	1323744	type	True	80.2056	553	1048	95	below_threshold
Pseudomonas profundi	strain=M5	GCA_008638305.1	1981513	1981513	type	True	78.3126	240	1048	95	below_threshold
Halopseudomonas litoralis	strain=2SM5	GCA_900105005.1	797277	797277	type	True	78.1291	233	1048	95	below_threshold
Pseudomonas saliphila	strain=16W4-4-3	GCA_008638345.1	2586906	2586906	type	True	78.1277	266	1048	95	below_threshold
Halopseudomonas bauzanensis	strain=DSM 22558	GCA_900111225.1	653930	653930	type	True	77.955	239	1048	95	below_threshold
Halopseudomonas pachastrellae	strain=JCM 12285	GCA_900114765.1	254161	254161	type	True	77.7248	270	1048	95	below_threshold
Halopseudomonas pachastrellae	strain=CCUG 46540	GCA_001989375.1	254161	254161	type	True	77.6599	265	1048	95	below_threshold
Pseudomonas syringae group genomosp. 7	strain=ICMP 4091	GCA_022557255.1	251699	251699	pathovar	True	76.9939	87	1048	95	below_threshold
Pseudomonas nabeulensis	strain=E10B	GCA_004682045.1	2293833	2293833	type	True	76.9347	95	1048	95	below_threshold
Pseudomonas cichorii	strain=DSM 50259	GCA_018343775.1	36746	36746	suspected-type	True	76.9332	99	1048	95	below_threshold
Pseudomonas edaphica	strain=RD25	GCA_005863185.1	2006980	2006980	type	True	76.9328	90	1048	95	below_threshold
Pseudomonas cichorii	strain=ATCC 10857	GCA_900104015.1	36746	36746	suspected-type	True	76.9287	101	1048	95	below_threshold
Pseudomonas simiae	strain=CCUG 50988	GCA_001730615.1	321846	321846	type	True	76.9208	102	1048	95	below_threshold
Pseudomonas kilonensis	strain=DSM 13647	GCA_001269885.1	132476	132476	type	True	76.7908	107	1048	95	below_threshold
Pseudomonas simiae	strain=CCUG 50988	GCA_900111895.1	321846	321846	type	True	76.7855	102	1048	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	76.7852	137	1048	95	below_threshold
Pseudomonas cichorii	strain=LMG 2162	GCA_015471425.1	36746	36746	suspected-type	True	76.7722	100	1048	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_024448335.1	2968969	2968969	type	True	76.7522	136	1048	95	below_threshold
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	76.7501	137	1048	95	below_threshold
Pseudomonas rhizophila	strain=S211	GCA_003033885.1	2045200	2045200	type	True	76.7113	119	1048	95	below_threshold
Pseudomonas paraversuta	strain=V4/DAB/S4/2a	GCA_904063065.1	2750624	2750624	type	True	76.4155	90	1048	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 11:51:55,602] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41046/tc_result.tsv
[2023-03-15 11:51:55,602] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:51:55,602] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:51:55,602] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2a1c7fa0-4376-42dd-8bbd-10ff60d2adfc/dqc_reference/checkm_data
[2023-03-15 11:51:55,603] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:51:55,609] [INFO] Task started: CheckM
[2023-03-15 11:51:55,609] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41046/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41046/checkm_input OceanDNA-b41046/checkm_result
[2023-03-15 11:52:45,760] [INFO] Task succeeded: CheckM
[2023-03-15 11:52:45,760] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:52:46,336] [INFO] ===== Completeness check finished =====
[2023-03-15 11:52:46,337] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:52:46,337] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41046/markers.fasta)
[2023-03-15 11:52:46,338] [INFO] Task started: Blastn
[2023-03-15 11:52:46,338] [INFO] Running command: blastn -query OceanDNA-b41046/markers.fasta -db /var/lib/cwl/stg2a1c7fa0-4376-42dd-8bbd-10ff60d2adfc/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41046/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:52:47,544] [INFO] Task succeeded: Blastn
[2023-03-15 11:52:47,544] [INFO] Selected 14 target genomes.
[2023-03-15 11:52:47,544] [INFO] Target genome list was writen to OceanDNA-b41046/target_genomes_gtdb.txt
[2023-03-15 11:52:47,557] [INFO] Task started: fastANI
[2023-03-15 11:52:47,558] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f30cbe4-59b4-45e4-a562-443edd7f5125/OceanDNA-b41046.fa --refList OceanDNA-b41046/target_genomes_gtdb.txt --output OceanDNA-b41046/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:52:56,614] [INFO] Task succeeded: fastANI
[2023-03-15 11:52:56,623] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 11:52:56,623] [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_008641105.1	s__Pseudomonas_D salina	80.2207	554	1048	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	100.00	100.00	0.99	0.99	2	-
GCA_016763285.1	s__Pseudomonas_D sp016763285	79.3789	425	1048	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009497895.1	s__Pseudomonas_D pelagia_A	79.2475	414	1048	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000410875.1	s__Pseudomonas_D pelagia	79.1161	385	1048	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008365385.1	s__Pseudomonas_D laoshanensis	78.9451	408	1048	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	96.00	95.95	0.96	0.95	3	-
GCA_002840055.1	s__Pseudomonas_D sp002840055	78.2589	241	1048	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012844345.1	s__Pseudomonas_D sp012844345	78.1698	244	1048	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008638345.1	s__Pseudomonas_D saliphila	78.123	267	1048	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002979975.1	s__Pseudomonas_D sp002979975	77.9609	247	1048	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105655.1	s__Pseudomonas_D salegens	77.8431	248	1048	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105255.1	s__Pseudomonas_D sabulinigri	77.8244	283	1048	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007117785.1	s__Pseudomonas_D sp007117785	77.7519	168	1048	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007692485.1	s__Pseudomonas_D sp007692485	77.6119	190	1048	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003444685.1	s__Pseudomonas_D gallaeciensis	77.6016	272	1048	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	97.87	97.82	0.88	0.85	8	-
--------------------------------------------------------------------------------
[2023-03-15 11:52:56,623] [INFO] GTDB search result was written to OceanDNA-b41046/result_gtdb.tsv
[2023-03-15 11:52:56,623] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:52:56,625] [INFO] DFAST_QC result json was written to OceanDNA-b41046/dqc_result.json
[2023-03-15 11:52:56,625] [INFO] DFAST_QC completed!
[2023-03-15 11:52:56,625] [INFO] Total running time: 0h1m39s