[2024-01-24 13:36:44,403] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:44,404] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:44,405] [INFO] DQC Reference Directory: /var/lib/cwl/stg3a5a7063-b2df-48de-a80b-b0a900b27d6b/dqc_reference
[2024-01-24 13:36:45,783] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:45,784] [INFO] Task started: Prodigal
[2024-01-24 13:36:45,785] [INFO] Running command: gunzip -c /var/lib/cwl/stg183f97e0-2304-4f6d-9530-913267a3499b/GCF_021602585.1_ASM2160258v1_genomic.fna.gz | prodigal -d GCF_021602585.1_ASM2160258v1_genomic.fna/cds.fna -a GCF_021602585.1_ASM2160258v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:05,469] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:05,470] [INFO] Task started: HMMsearch
[2024-01-24 13:37:05,470] [INFO] Running command: hmmsearch --tblout GCF_021602585.1_ASM2160258v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3a5a7063-b2df-48de-a80b-b0a900b27d6b/dqc_reference/reference_markers.hmm GCF_021602585.1_ASM2160258v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:05,749] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:05,750] [INFO] Found 6/6 markers.
[2024-01-24 13:37:05,799] [INFO] Query marker FASTA was written to GCF_021602585.1_ASM2160258v1_genomic.fna/markers.fasta
[2024-01-24 13:37:05,799] [INFO] Task started: Blastn
[2024-01-24 13:37:05,799] [INFO] Running command: blastn -query GCF_021602585.1_ASM2160258v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a5a7063-b2df-48de-a80b-b0a900b27d6b/dqc_reference/reference_markers.fasta -out GCF_021602585.1_ASM2160258v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:06,996] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:06,999] [INFO] Selected 14 target genomes.
[2024-01-24 13:37:07,000] [INFO] Target genome list was writen to GCF_021602585.1_ASM2160258v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:07,012] [INFO] Task started: fastANI
[2024-01-24 13:37:07,012] [INFO] Running command: fastANI --query /var/lib/cwl/stg183f97e0-2304-4f6d-9530-913267a3499b/GCF_021602585.1_ASM2160258v1_genomic.fna.gz --refList GCF_021602585.1_ASM2160258v1_genomic.fna/target_genomes.txt --output GCF_021602585.1_ASM2160258v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:28,001] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:28,002] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3a5a7063-b2df-48de-a80b-b0a900b27d6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:28,002] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3a5a7063-b2df-48de-a80b-b0a900b27d6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:28,015] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:37:28,015] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:28,016] [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	100.0	1930	1932	95	conclusive
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	99.9578	1784	1932	95	conclusive
Pseudomonas plecoglossicida	strain=NBRC 103162	GCA_000730665.1	70775	70775	suspected-type	True	90.5893	1433	1932	95	below_threshold
Pseudomonas plecoglossicida	strain=DSM 15088	GCA_000688275.1	70775	70775	suspected-type	True	90.567	1450	1932	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_021602465.1	2740517	2740517	suspected-type	True	88.6226	1432	1932	95	below_threshold
Pseudomonas ceruminis	strain=BML-PP028	GCA_021602025.1	2740516	2740516	type	True	88.2607	1402	1932	95	below_threshold
Pseudomonas ceruminis	strain=BML-PP028	GCA_013373895.1	2740516	2740516	type	True	88.253	1397	1932	95	below_threshold
Pseudomonas anuradhapurensis	strain=RD8MR3	GCA_014269225.2	485870	485870	type	True	88.0919	1342	1932	95	below_threshold
Pseudomonas muyukensis	strain=COW39	GCA_019139535.1	2842357	2842357	type	True	87.9349	1326	1932	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	87.9287	1294	1932	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_000731675.1	1495066	1495066	type	True	87.8809	1422	1932	95	below_threshold
Pseudomonas sichuanensis	strain=WCHPs060039	GCA_003231305.1	2213015	2213015	type	True	87.799	1348	1932	95	below_threshold
Pseudomonas oryziphila	strain=1257	GCA_003940825.1	2894079	2894079	type	True	87.7494	1378	1932	95	below_threshold
Pseudomonas kermanshahensis	strain=SWRI100	GCA_014269205.2	2745482	2745482	type	True	87.6787	1417	1932	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:28,020] [INFO] DFAST Taxonomy check result was written to GCF_021602585.1_ASM2160258v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:28,021] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:28,021] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:28,021] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3a5a7063-b2df-48de-a80b-b0a900b27d6b/dqc_reference/checkm_data
[2024-01-24 13:37:28,023] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:28,116] [INFO] Task started: CheckM
[2024-01-24 13:37:28,117] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021602585.1_ASM2160258v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021602585.1_ASM2160258v1_genomic.fna/checkm_input GCF_021602585.1_ASM2160258v1_genomic.fna/checkm_result
[2024-01-24 13:38:30,870] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:30,871] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:30,890] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:30,890] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:30,890] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021602585.1_ASM2160258v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:30,890] [INFO] Task started: Blastn
[2024-01-24 13:38:30,890] [INFO] Running command: blastn -query GCF_021602585.1_ASM2160258v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a5a7063-b2df-48de-a80b-b0a900b27d6b/dqc_reference/reference_markers_gtdb.fasta -out GCF_021602585.1_ASM2160258v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:32,963] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:32,966] [INFO] Selected 14 target genomes.
[2024-01-24 13:38:32,967] [INFO] Target genome list was writen to GCF_021602585.1_ASM2160258v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:32,987] [INFO] Task started: fastANI
[2024-01-24 13:38:32,987] [INFO] Running command: fastANI --query /var/lib/cwl/stg183f97e0-2304-4f6d-9530-913267a3499b/GCF_021602585.1_ASM2160258v1_genomic.fna.gz --refList GCF_021602585.1_ASM2160258v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021602585.1_ASM2160258v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:52,846] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:52,858] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:52,858] [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_013373935.1	s__Pseudomonas_E sp002438125	99.9578	1784	1932	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.14	98.14	0.84	0.84	2	conclusive
GCF_000282535.1	s__Pseudomonas_E sp000282535	91.1581	1399	1932	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	90.5968	1432	1932	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_002112505.1	s__Pseudomonas_E sp002112505	89.3965	1510	1932	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	0.99	6	-
GCA_017744435.1	s__Pseudomonas_E sp017744435	89.2923	1464	1932	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_003331055.1	s__Pseudomonas_E sp003331055	88.4491	1307	1932	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_012975065.1	s__Pseudomonas_E sp012975065	88.2171	1355	1932	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.79	97.74	0.94	0.94	3	-
GCF_001320525.1	s__Pseudomonas_E sp001320525	88.143	1401	1932	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.10	98.78	0.89	0.86	10	-
GCF_000019445.1	s__Pseudomonas_E putida_E	87.9369	1392	1932	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.71	96.19	0.87	0.82	12	-
GCF_000731675.1	s__Pseudomonas_E capeferrum	87.9133	1418	1932	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.03	98.55	0.93	0.90	7	-
GCF_015354575.1	s__Pseudomonas_E sp015354575	87.8829	1382	1932	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_005080685.1	s__Pseudomonas_E putida_V	87.8157	1353	1932	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	87.812	1347	1932	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_002736125.1	s__Pseudomonas_E putida_M	87.7343	1429	1932	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.41	97.25	0.91	0.90	8	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:52,860] [INFO] GTDB search result was written to GCF_021602585.1_ASM2160258v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:52,861] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:52,864] [INFO] DFAST_QC result json was written to GCF_021602585.1_ASM2160258v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:52,864] [INFO] DFAST_QC completed!
[2024-01-24 13:38:52,864] [INFO] Total running time: 0h2m8s