[2023-03-16 14:26:34,024] [INFO] DFAST_QC pipeline started.
[2023-03-16 14:26:34,025] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 14:26:34,025] [INFO] DQC Reference Directory: /var/lib/cwl/stg3cb13db8-1d9f-48b7-865e-e37eff7d30e7/dqc_reference
[2023-03-16 14:26:35,438] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 14:26:35,439] [INFO] Task started: Prodigal
[2023-03-16 14:26:35,439] [INFO] Running command: cat /var/lib/cwl/stgd5850e8a-5184-4b5b-8032-36b570693fc1/OceanDNA-b41014.fa | prodigal -d OceanDNA-b41014/cds.fna -a OceanDNA-b41014/protein.faa -g 11 -q > /dev/null
[2023-03-16 14:26:51,741] [INFO] Task succeeded: Prodigal
[2023-03-16 14:26:51,741] [INFO] Task started: HMMsearch
[2023-03-16 14:26:51,741] [INFO] Running command: hmmsearch --tblout OceanDNA-b41014/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3cb13db8-1d9f-48b7-865e-e37eff7d30e7/dqc_reference/reference_markers.hmm OceanDNA-b41014/protein.faa > /dev/null
[2023-03-16 14:26:51,945] [INFO] Task succeeded: HMMsearch
[2023-03-16 14:26:51,946] [INFO] Found 6/6 markers.
[2023-03-16 14:26:51,967] [INFO] Query marker FASTA was written to OceanDNA-b41014/markers.fasta
[2023-03-16 14:26:51,968] [INFO] Task started: Blastn
[2023-03-16 14:26:51,968] [INFO] Running command: blastn -query OceanDNA-b41014/markers.fasta -db /var/lib/cwl/stg3cb13db8-1d9f-48b7-865e-e37eff7d30e7/dqc_reference/reference_markers.fasta -out OceanDNA-b41014/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 14:26:53,001] [INFO] Task succeeded: Blastn
[2023-03-16 14:26:53,002] [INFO] Selected 13 target genomes.
[2023-03-16 14:26:53,002] [INFO] Target genome list was writen to OceanDNA-b41014/target_genomes.txt
[2023-03-16 14:26:53,010] [INFO] Task started: fastANI
[2023-03-16 14:26:53,011] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5850e8a-5184-4b5b-8032-36b570693fc1/OceanDNA-b41014.fa --refList OceanDNA-b41014/target_genomes.txt --output OceanDNA-b41014/fastani_result.tsv --threads 1
[2023-03-16 14:27:02,694] [INFO] Task succeeded: fastANI
[2023-03-16 14:27:02,695] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3cb13db8-1d9f-48b7-865e-e37eff7d30e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 14:27:02,695] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3cb13db8-1d9f-48b7-865e-e37eff7d30e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 14:27:02,917] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 14:27:02,917] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 14:27:02,917] [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 pachastrellae	strain=JCM 12285	GCA_900114765.1	254161	254161	type	True	93.2483	755	855	95	below_threshold
Halopseudomonas pachastrellae	strain=CCUG 46540	GCA_001989375.1	254161	254161	type	True	93.2041	747	855	95	below_threshold
Halopseudomonas oceani	strain=CGMCC 1.15195	GCA_014641295.1	1708783	1708783	type	True	83.5299	640	855	95	below_threshold
Halopseudomonas oceani	strain=DSM 100277	GCA_002903165.1	1708783	1708783	type	True	83.5023	632	855	95	below_threshold
Halopseudomonas aestusnigri	strain=CECT 8317	GCA_900108005.1	857252	857252	type	True	83.0132	597	855	95	below_threshold
Halopseudomonas aestusnigri	strain=VGXO14	GCA_002197985.1	857252	857252	type	True	82.9902	606	855	95	below_threshold
Pseudomonas alcaligenes	strain=NCTC10367	GCA_900455475.1	43263	43263	type	True	78.2212	284	855	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	78.2138	233	855	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	78.2069	261	855	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	78.0566	287	855	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	78.0495	226	855	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	78.0168	230	855	95	below_threshold
Pseudomonas mangrovi	strain=TC11	GCA_003052585.1	2161748	2161748	type	True	77.7983	240	855	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 14:27:02,917] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41014/tc_result.tsv
[2023-03-16 14:27:02,918] [INFO] ===== Taxonomy check completed =====
[2023-03-16 14:27:02,918] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 14:27:02,918] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3cb13db8-1d9f-48b7-865e-e37eff7d30e7/dqc_reference/checkm_data
[2023-03-16 14:27:02,919] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 14:27:02,943] [INFO] Task started: CheckM
[2023-03-16 14:27:02,943] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41014/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41014/checkm_input OceanDNA-b41014/checkm_result
[2023-03-16 14:27:51,900] [INFO] Task succeeded: CheckM
[2023-03-16 14:27:51,900] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.73%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 14:27:51,902] [INFO] ===== Completeness check finished =====
[2023-03-16 14:27:51,903] [INFO] ===== Start GTDB Search =====
[2023-03-16 14:27:51,903] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41014/markers.fasta)
[2023-03-16 14:27:51,904] [INFO] Task started: Blastn
[2023-03-16 14:27:51,904] [INFO] Running command: blastn -query OceanDNA-b41014/markers.fasta -db /var/lib/cwl/stg3cb13db8-1d9f-48b7-865e-e37eff7d30e7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41014/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 14:27:53,690] [INFO] Task succeeded: Blastn
[2023-03-16 14:27:53,691] [INFO] Selected 10 target genomes.
[2023-03-16 14:27:53,691] [INFO] Target genome list was writen to OceanDNA-b41014/target_genomes_gtdb.txt
[2023-03-16 14:27:53,933] [INFO] Task started: fastANI
[2023-03-16 14:27:53,934] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5850e8a-5184-4b5b-8032-36b570693fc1/OceanDNA-b41014.fa --refList OceanDNA-b41014/target_genomes_gtdb.txt --output OceanDNA-b41014/fastani_result_gtdb.tsv --threads 1
[2023-03-16 14:28:01,475] [INFO] Task succeeded: fastANI
[2023-03-16 14:28:01,482] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 14:28:01,482] [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_900114765.1	s__Pseudomonas_D pachastrellae	93.2483	755	855	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	96.15	95.72	0.86	0.72	17	-
GCF_003444685.1	s__Pseudomonas_D gallaeciensis	90.6207	803	855	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	97.87	97.82	0.88	0.85	8	-
GCA_002296055.1	s__Pseudomonas_D sp002296055	86.3101	639	855	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_002903165.1	s__Pseudomonas_D oceani	83.474	635	855	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002197985.1	s__Pseudomonas_D aestusnigri	82.98	607	855	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	97.11	96.74	0.91	0.81	25	-
GCF_003797905.1	s__Pseudomonas_D sp002683975	78.9635	369	855	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	98.94	98.05	0.94	0.90	5	-
GCF_014219065.1	s__Pseudomonas_D xiamenensis	78.8208	354	855	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	78.7403	345	855	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_900105005.1	s__Pseudomonas_D litoralis	78.6485	263	855	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_900115905.1	s__Pseudomonas_D formosensis	78.6358	294	855	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	98.74	98.74	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-03-16 14:28:01,482] [INFO] GTDB search result was written to OceanDNA-b41014/result_gtdb.tsv
[2023-03-16 14:28:01,483] [INFO] ===== GTDB Search completed =====
[2023-03-16 14:28:01,484] [INFO] DFAST_QC result json was written to OceanDNA-b41014/dqc_result.json
[2023-03-16 14:28:01,484] [INFO] DFAST_QC completed!
[2023-03-16 14:28:01,484] [INFO] Total running time: 0h1m27s