[2024-01-24 11:51:49,803] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:49,805] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:49,805] [INFO] DQC Reference Directory: /var/lib/cwl/stg05af7d7a-f5a6-4a61-83c8-a6ffbdb145b6/dqc_reference
[2024-01-24 11:51:51,029] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:51,030] [INFO] Task started: Prodigal
[2024-01-24 11:51:51,030] [INFO] Running command: gunzip -c /var/lib/cwl/stg33779c93-2066-46fb-afec-43db0819e92e/GCF_014268935.2_ASM1426893v2_genomic.fna.gz | prodigal -d GCF_014268935.2_ASM1426893v2_genomic.fna/cds.fna -a GCF_014268935.2_ASM1426893v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:52:10,414] [INFO] Task succeeded: Prodigal
[2024-01-24 11:52:10,415] [INFO] Task started: HMMsearch
[2024-01-24 11:52:10,415] [INFO] Running command: hmmsearch --tblout GCF_014268935.2_ASM1426893v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg05af7d7a-f5a6-4a61-83c8-a6ffbdb145b6/dqc_reference/reference_markers.hmm GCF_014268935.2_ASM1426893v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:52:10,712] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:52:10,713] [INFO] Found 6/6 markers.
[2024-01-24 11:52:10,765] [INFO] Query marker FASTA was written to GCF_014268935.2_ASM1426893v2_genomic.fna/markers.fasta
[2024-01-24 11:52:10,766] [INFO] Task started: Blastn
[2024-01-24 11:52:10,766] [INFO] Running command: blastn -query GCF_014268935.2_ASM1426893v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg05af7d7a-f5a6-4a61-83c8-a6ffbdb145b6/dqc_reference/reference_markers.fasta -out GCF_014268935.2_ASM1426893v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:11,881] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:11,885] [INFO] Selected 17 target genomes.
[2024-01-24 11:52:11,886] [INFO] Target genome list was writen to GCF_014268935.2_ASM1426893v2_genomic.fna/target_genomes.txt
[2024-01-24 11:52:11,896] [INFO] Task started: fastANI
[2024-01-24 11:52:11,896] [INFO] Running command: fastANI --query /var/lib/cwl/stg33779c93-2066-46fb-afec-43db0819e92e/GCF_014268935.2_ASM1426893v2_genomic.fna.gz --refList GCF_014268935.2_ASM1426893v2_genomic.fna/target_genomes.txt --output GCF_014268935.2_ASM1426893v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:38,655] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:38,656] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg05af7d7a-f5a6-4a61-83c8-a6ffbdb145b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:38,656] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg05af7d7a-f5a6-4a61-83c8-a6ffbdb145b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:38,682] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:52:38,682] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:52:38,682] [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 mosselii	strain=DSM 17497	GCA_019823065.1	78327	78327	type	True	94.6924	1678	1968	95	below_threshold
Pseudomonas mosselii	strain=DSM 17497	GCA_000621225.1	78327	78327	type	True	94.6549	1658	1968	95	below_threshold
Pseudomonas maumuensis	strain=COW77	GCA_019139675.1	2842354	2842354	type	True	91.696	1632	1968	95	below_threshold
Pseudomonas soli	strain=LMG 27941	GCA_900110655.1	1306993	1306993	type	True	91.4104	1598	1968	95	below_threshold
Pseudomonas muyukensis	strain=COW39	GCA_019139535.1	2842357	2842357	type	True	90.4211	1524	1968	95	below_threshold
Pseudomonas xantholysinigenes	strain=RW9S1A	GCA_014268885.2	2745490	2745490	type	True	90.3393	1537	1968	95	below_threshold
Pseudomonas entomophila	strain=L48	GCA_000026105.1	312306	312306	suspected-type	True	89.9095	1566	1968	95	below_threshold
Pseudomonas sichuanensis	strain=WCHPs060039	GCA_003231305.1	2213015	2213015	type	True	89.2956	1417	1968	95	below_threshold
Pseudomonas oryziphila	strain=1257	GCA_003940825.1	2894079	2894079	type	True	89.2554	1448	1968	95	below_threshold
Pseudomonas inefficax	strain=JV551A3	GCA_900277125.1	2078786	2078786	type	True	87.1629	1320	1968	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_021602465.1	2740517	2740517	suspected-type	True	86.9397	1310	1968	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_013373915.1	2740517	2740517	suspected-type	True	86.731	1297	1968	95	below_threshold
Pseudomonas monteilii	strain=DSM 14164	GCA_000621245.1	76759	76759	type	True	86.3759	1284	1968	95	below_threshold
Pseudomonas monteilii	strain=NBRC 103158	GCA_000730605.1	76759	76759	type	True	86.3401	1264	1968	95	below_threshold
Pseudomonas bharatica	strain=CSV86	GCA_000319305.2	2692112	2692112	type	True	84.5781	1239	1968	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	82.5706	847	1968	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	82.1893	874	1968	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:38,684] [INFO] DFAST Taxonomy check result was written to GCF_014268935.2_ASM1426893v2_genomic.fna/tc_result.tsv
[2024-01-24 11:52:38,685] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:38,685] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:38,685] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg05af7d7a-f5a6-4a61-83c8-a6ffbdb145b6/dqc_reference/checkm_data
[2024-01-24 11:52:38,686] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:38,743] [INFO] Task started: CheckM
[2024-01-24 11:52:38,743] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014268935.2_ASM1426893v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014268935.2_ASM1426893v2_genomic.fna/checkm_input GCF_014268935.2_ASM1426893v2_genomic.fna/checkm_result
[2024-01-24 11:53:37,587] [INFO] Task succeeded: CheckM
[2024-01-24 11:53:37,589] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:53:37,609] [INFO] ===== Completeness check finished =====
[2024-01-24 11:53:37,609] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:53:37,610] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014268935.2_ASM1426893v2_genomic.fna/markers.fasta)
[2024-01-24 11:53:37,610] [INFO] Task started: Blastn
[2024-01-24 11:53:37,610] [INFO] Running command: blastn -query GCF_014268935.2_ASM1426893v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg05af7d7a-f5a6-4a61-83c8-a6ffbdb145b6/dqc_reference/reference_markers_gtdb.fasta -out GCF_014268935.2_ASM1426893v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:53:39,735] [INFO] Task succeeded: Blastn
[2024-01-24 11:53:39,740] [INFO] Selected 11 target genomes.
[2024-01-24 11:53:39,740] [INFO] Target genome list was writen to GCF_014268935.2_ASM1426893v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:53:39,748] [INFO] Task started: fastANI
[2024-01-24 11:53:39,748] [INFO] Running command: fastANI --query /var/lib/cwl/stg33779c93-2066-46fb-afec-43db0819e92e/GCF_014268935.2_ASM1426893v2_genomic.fna.gz --refList GCF_014268935.2_ASM1426893v2_genomic.fna/target_genomes_gtdb.txt --output GCF_014268935.2_ASM1426893v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:54:01,526] [INFO] Task succeeded: fastANI
[2024-01-24 11:54:01,546] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:54:01,547] [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_016861355.1	s__Pseudomonas_E sp001259595	95.6524	1744	1968	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.3017	95.65	95.59	0.90	0.88	5	conclusive
GCF_003205295.1	s__Pseudomonas_E mosselii_B	94.7859	1642	1968	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.3017	N/A	N/A	N/A	N/A	1	-
GCF_000621225.1	s__Pseudomonas_E mosselii	94.6427	1659	1968	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.55	97.48	0.92	0.90	14	-
GCF_019139675.1	s__Pseudomonas_E sp019139675	91.7082	1632	1968	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_900110655.1	s__Pseudomonas_E soli	91.4208	1597	1968	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.13	95.09	0.90	0.88	23	-
GCF_019139535.1	s__Pseudomonas_E sp019139535	90.4203	1523	1968	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_014268885.2	s__Pseudomonas_E sp014268885	90.3328	1542	1968	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_018417595.1	s__Pseudomonas_E entomophila_C	89.969	1566	1968	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_003231305.1	s__Pseudomonas_E sichuanensis	89.3311	1413	1968	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.11	95.79	0.86	0.83	4	-
GCF_001642705.1	s__Pseudomonas_E sp001642705	87.3443	1338	1968	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_900277125.1	s__Pseudomonas_E inefficax	87.1457	1320	1968	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.83	97.08	0.92	0.89	5	-
--------------------------------------------------------------------------------
[2024-01-24 11:54:01,549] [INFO] GTDB search result was written to GCF_014268935.2_ASM1426893v2_genomic.fna/result_gtdb.tsv
[2024-01-24 11:54:01,550] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:54:01,556] [INFO] DFAST_QC result json was written to GCF_014268935.2_ASM1426893v2_genomic.fna/dqc_result.json
[2024-01-24 11:54:01,556] [INFO] DFAST_QC completed!
[2024-01-24 11:54:01,557] [INFO] Total running time: 0h2m12s