[2024-01-24 14:14:45,009] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:45,013] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:45,014] [INFO] DQC Reference Directory: /var/lib/cwl/stgd785ae8d-ced6-4efc-a644-5d7c9aa25aab/dqc_reference
[2024-01-24 14:14:46,366] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:46,367] [INFO] Task started: Prodigal
[2024-01-24 14:14:46,368] [INFO] Running command: gunzip -c /var/lib/cwl/stge07d1255-bc2c-42fe-8259-b509b6dac034/GCF_014269185.2_ASM1426918v2_genomic.fna.gz | prodigal -d GCF_014269185.2_ASM1426918v2_genomic.fna/cds.fna -a GCF_014269185.2_ASM1426918v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:15:03,964] [INFO] Task succeeded: Prodigal
[2024-01-24 14:15:03,965] [INFO] Task started: HMMsearch
[2024-01-24 14:15:03,965] [INFO] Running command: hmmsearch --tblout GCF_014269185.2_ASM1426918v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd785ae8d-ced6-4efc-a644-5d7c9aa25aab/dqc_reference/reference_markers.hmm GCF_014269185.2_ASM1426918v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:15:04,247] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:15:04,248] [INFO] Found 6/6 markers.
[2024-01-24 14:15:04,301] [INFO] Query marker FASTA was written to GCF_014269185.2_ASM1426918v2_genomic.fna/markers.fasta
[2024-01-24 14:15:04,301] [INFO] Task started: Blastn
[2024-01-24 14:15:04,301] [INFO] Running command: blastn -query GCF_014269185.2_ASM1426918v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgd785ae8d-ced6-4efc-a644-5d7c9aa25aab/dqc_reference/reference_markers.fasta -out GCF_014269185.2_ASM1426918v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:05,353] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:05,356] [INFO] Selected 14 target genomes.
[2024-01-24 14:15:05,356] [INFO] Target genome list was writen to GCF_014269185.2_ASM1426918v2_genomic.fna/target_genomes.txt
[2024-01-24 14:15:05,365] [INFO] Task started: fastANI
[2024-01-24 14:15:05,365] [INFO] Running command: fastANI --query /var/lib/cwl/stge07d1255-bc2c-42fe-8259-b509b6dac034/GCF_014269185.2_ASM1426918v2_genomic.fna.gz --refList GCF_014269185.2_ASM1426918v2_genomic.fna/target_genomes.txt --output GCF_014269185.2_ASM1426918v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:24,830] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:24,831] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd785ae8d-ced6-4efc-a644-5d7c9aa25aab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:24,831] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd785ae8d-ced6-4efc-a644-5d7c9aa25aab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:24,846] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:15:24,846] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:15:24,846] [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 oryzicola	strain=RD9SR1	GCA_014269185.2	485876	485876	type	True	100.0	1744	1745	95	inconclusive
Pseudomonas anuradhapurensis	strain=RD8MR3	GCA_014269225.2	485870	485870	type	True	95.1286	1578	1745	95	inconclusive
Pseudomonas inefficax	strain=JV551A3	GCA_900277125.1	2078786	2078786	type	True	90.6209	1445	1745	95	below_threshold
Pseudomonas putida	strain=ATCC 12633	GCA_024508115.1	303	303	suspected-type	True	89.0908	1410	1745	95	below_threshold
Pseudomonas monteilii	strain=DSM 14164	GCA_000621245.1	76759	76759	type	True	88.9193	1406	1745	95	below_threshold
Pseudomonas monteilii	strain=NBRC 103158	GCA_000730605.1	76759	76759	type	True	88.904	1389	1745	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	87.7616	1257	1745	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	87.3529	1269	1745	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_000731675.1	1495066	1495066	type	True	87.309	1373	1745	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_021602465.1	2740517	2740517	suspected-type	True	87.2705	1352	1745	95	below_threshold
Pseudomonas plecoglossicida	strain=DSM 15088	GCA_000688275.1	70775	70775	suspected-type	True	87.2447	1262	1745	95	below_threshold
Pseudomonas plecoglossicida	strain=NBRC 103162	GCA_000730665.1	70775	70775	suspected-type	True	87.2019	1250	1745	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_013373915.1	2740517	2740517	suspected-type	True	87.1741	1330	1745	95	below_threshold
Pseudomonas muyukensis	strain=COW39	GCA_019139535.1	2842357	2842357	type	True	86.7093	1277	1745	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:24,848] [INFO] DFAST Taxonomy check result was written to GCF_014269185.2_ASM1426918v2_genomic.fna/tc_result.tsv
[2024-01-24 14:15:24,849] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:24,849] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:24,849] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd785ae8d-ced6-4efc-a644-5d7c9aa25aab/dqc_reference/checkm_data
[2024-01-24 14:15:24,850] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:24,899] [INFO] Task started: CheckM
[2024-01-24 14:15:24,900] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014269185.2_ASM1426918v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014269185.2_ASM1426918v2_genomic.fna/checkm_input GCF_014269185.2_ASM1426918v2_genomic.fna/checkm_result
[2024-01-24 14:16:19,439] [INFO] Task succeeded: CheckM
[2024-01-24 14:16:19,440] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:16:19,461] [INFO] ===== Completeness check finished =====
[2024-01-24 14:16:19,461] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:16:19,462] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014269185.2_ASM1426918v2_genomic.fna/markers.fasta)
[2024-01-24 14:16:19,462] [INFO] Task started: Blastn
[2024-01-24 14:16:19,462] [INFO] Running command: blastn -query GCF_014269185.2_ASM1426918v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgd785ae8d-ced6-4efc-a644-5d7c9aa25aab/dqc_reference/reference_markers_gtdb.fasta -out GCF_014269185.2_ASM1426918v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:16:21,517] [INFO] Task succeeded: Blastn
[2024-01-24 14:16:21,521] [INFO] Selected 12 target genomes.
[2024-01-24 14:16:21,522] [INFO] Target genome list was writen to GCF_014269185.2_ASM1426918v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:16:21,550] [INFO] Task started: fastANI
[2024-01-24 14:16:21,550] [INFO] Running command: fastANI --query /var/lib/cwl/stge07d1255-bc2c-42fe-8259-b509b6dac034/GCF_014269185.2_ASM1426918v2_genomic.fna.gz --refList GCF_014269185.2_ASM1426918v2_genomic.fna/target_genomes_gtdb.txt --output GCF_014269185.2_ASM1426918v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:16:39,782] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:39,793] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:16:39,793] [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_014269185.2	s__Pseudomonas_E sp014269185	100.0	1744	1745	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_012975065.1	s__Pseudomonas_E sp012975065	94.8665	1590	1745	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.79	97.74	0.94	0.94	3	-
GCA_002386445.1	s__Pseudomonas_E sp002386445	92.6405	1459	1745	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	91.0207	1476	1745	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_009932335.1	s__Pseudomonas_E asiatica	90.867	1478	1745	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0481	97.98	96.05	0.89	0.79	58	-
GCF_015680405.1	s__Pseudomonas_E pudica	90.6707	1433	1745	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_002165135.1	s__Pseudomonas_E sp002165135	90.653	1430	1745	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_900277125.1	s__Pseudomonas_E inefficax	90.6128	1446	1745	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.83	97.08	0.92	0.89	5	-
GCF_002113165.1	s__Pseudomonas_E sp002113165	90.5278	1458	1745	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	3	-
GCF_003331055.1	s__Pseudomonas_E sp003331055	90.2787	1392	1745	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_000935045.1	s__Pseudomonas_E sp000935045	89.9895	1356	1745	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_000730665.1	s__Pseudomonas_E plecoglossicida	87.227	1246	1745	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.81	99.74	0.97	0.95	6	-
--------------------------------------------------------------------------------
[2024-01-24 14:16:39,795] [INFO] GTDB search result was written to GCF_014269185.2_ASM1426918v2_genomic.fna/result_gtdb.tsv
[2024-01-24 14:16:39,795] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:16:39,799] [INFO] DFAST_QC result json was written to GCF_014269185.2_ASM1426918v2_genomic.fna/dqc_result.json
[2024-01-24 14:16:39,799] [INFO] DFAST_QC completed!
[2024-01-24 14:16:39,799] [INFO] Total running time: 0h1m55s