[2024-01-24 11:34:52,779] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:52,782] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:52,782] [INFO] DQC Reference Directory: /var/lib/cwl/stg9d212126-b888-4c37-b387-6d77ebd1ccb0/dqc_reference
[2024-01-24 11:34:55,644] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:55,645] [INFO] Task started: Prodigal
[2024-01-24 11:34:55,646] [INFO] Running command: gunzip -c /var/lib/cwl/stg53075a75-0d62-47c4-b263-3a6c02408998/GCF_024112395.1_ASM2411239v1_genomic.fna.gz | prodigal -d GCF_024112395.1_ASM2411239v1_genomic.fna/cds.fna -a GCF_024112395.1_ASM2411239v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:20,132] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:20,133] [INFO] Task started: HMMsearch
[2024-01-24 11:35:20,133] [INFO] Running command: hmmsearch --tblout GCF_024112395.1_ASM2411239v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9d212126-b888-4c37-b387-6d77ebd1ccb0/dqc_reference/reference_markers.hmm GCF_024112395.1_ASM2411239v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:20,471] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:20,473] [INFO] Found 6/6 markers.
[2024-01-24 11:35:20,529] [INFO] Query marker FASTA was written to GCF_024112395.1_ASM2411239v1_genomic.fna/markers.fasta
[2024-01-24 11:35:20,529] [INFO] Task started: Blastn
[2024-01-24 11:35:20,529] [INFO] Running command: blastn -query GCF_024112395.1_ASM2411239v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d212126-b888-4c37-b387-6d77ebd1ccb0/dqc_reference/reference_markers.fasta -out GCF_024112395.1_ASM2411239v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:21,493] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:21,496] [INFO] Selected 14 target genomes.
[2024-01-24 11:35:21,497] [INFO] Target genome list was writen to GCF_024112395.1_ASM2411239v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:21,502] [INFO] Task started: fastANI
[2024-01-24 11:35:21,502] [INFO] Running command: fastANI --query /var/lib/cwl/stg53075a75-0d62-47c4-b263-3a6c02408998/GCF_024112395.1_ASM2411239v1_genomic.fna.gz --refList GCF_024112395.1_ASM2411239v1_genomic.fna/target_genomes.txt --output GCF_024112395.1_ASM2411239v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:46,627] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:46,628] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9d212126-b888-4c37-b387-6d77ebd1ccb0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:46,629] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9d212126-b888-4c37-b387-6d77ebd1ccb0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:46,644] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:46,645] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:46,645] [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 pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	100.0	2201	2203	95	conclusive
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	91.6281	1787	2203	95	below_threshold
Pseudomonas marginalis	strain=ICMP 3553	GCA_003700725.1	298	298	suspected-type	True	91.2263	1640	2203	95	below_threshold
Pseudomonas marginalis	strain=ICMP 3553	GCA_001645105.1	298	298	suspected-type	True	91.191	1756	2203	95	below_threshold
Pseudomonas azotoformans	strain=LMG 21611	GCA_900103345.1	47878	47878	suspected-type	True	91.1505	1863	2203	95	below_threshold
Pseudomonas azotoformans	strain=LMG 21611	GCA_001870415.1	47878	47878	suspected-type	True	91.1441	1847	2203	95	below_threshold
Pseudomonas azotoformans		GCA_900624915.1	47878	47878	suspected-type	True	91.1383	1842	2203	95	below_threshold
Pseudomonas azotoformans	strain=NBRC 12693	GCA_002091515.1	47878	47878	suspected-type	True	91.0956	1847	2203	95	below_threshold
Pseudomonas simiae	strain=CCUG 50988	GCA_900111895.1	321846	321846	type	True	90.8317	1729	2203	95	below_threshold
Pseudomonas simiae	strain=CCUG 50988	GCA_001730615.1	321846	321846	type	True	90.8102	1729	2203	95	below_threshold
Pseudomonas marginalis	strain=DSM 13124	GCA_007858155.1	298	298	suspected-type	True	89.1217	1693	2203	95	below_threshold
Pseudomonas fluorescens	strain=NCTC10038	GCA_900475215.1	294	294	suspected-type	True	87.8753	1676	2203	95	below_threshold
Pseudomonas spelaei	strain=CCM 7893	GCA_009724245.1	1055469	1055469	type	True	86.0579	1498	2203	95	below_threshold
Pseudomonas karstica	strain=CCM 7891	GCA_009707515.1	1055468	1055468	type	True	85.2413	1359	2203	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:46,646] [INFO] DFAST Taxonomy check result was written to GCF_024112395.1_ASM2411239v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:46,647] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:46,647] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:46,648] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9d212126-b888-4c37-b387-6d77ebd1ccb0/dqc_reference/checkm_data
[2024-01-24 11:35:46,649] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:46,707] [INFO] Task started: CheckM
[2024-01-24 11:35:46,708] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024112395.1_ASM2411239v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024112395.1_ASM2411239v1_genomic.fna/checkm_input GCF_024112395.1_ASM2411239v1_genomic.fna/checkm_result
[2024-01-24 11:36:57,579] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:57,580] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:57,602] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:57,602] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:57,603] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024112395.1_ASM2411239v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:57,603] [INFO] Task started: Blastn
[2024-01-24 11:36:57,603] [INFO] Running command: blastn -query GCF_024112395.1_ASM2411239v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d212126-b888-4c37-b387-6d77ebd1ccb0/dqc_reference/reference_markers_gtdb.fasta -out GCF_024112395.1_ASM2411239v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:59,269] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:59,274] [INFO] Selected 13 target genomes.
[2024-01-24 11:36:59,274] [INFO] Target genome list was writen to GCF_024112395.1_ASM2411239v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:59,284] [INFO] Task started: fastANI
[2024-01-24 11:36:59,284] [INFO] Running command: fastANI --query /var/lib/cwl/stg53075a75-0d62-47c4-b263-3a6c02408998/GCF_024112395.1_ASM2411239v1_genomic.fna.gz --refList GCF_024112395.1_ASM2411239v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024112395.1_ASM2411239v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:37:23,173] [INFO] Task succeeded: fastANI
[2024-01-24 11:37:23,201] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:37:23,202] [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_002007785.1	s__Pseudomonas_E azotoformans_B	99.0231	2073	2203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.95	98.86	0.94	0.92	6	conclusive
GCF_000612585.1	s__Pseudomonas_E sp000612585	92.5778	1729	2203	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_000503215.1	s__Pseudomonas_E canadensis	91.8666	1823	2203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.83	97.74	0.94	0.91	12	-
GCF_002563895.1	s__Pseudomonas_E lurida	91.6231	1788	2203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.19	99.03	0.94	0.91	25	-
GCF_001645105.1	s__Pseudomonas_E marginalis_B	91.1919	1756	2203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.70	98.28	0.91	0.87	10	-
GCF_900103345.1	s__Pseudomonas_E azotoformans	91.1459	1862	2203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.97	95.87	0.94	0.87	9	-
GCF_001870465.1	s__Pseudomonas_E extremorientalis	91.0925	1789	2203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.37	98.13	0.91	0.89	29	-
GCF_001579805.1	s__Pseudomonas_E azotoformans_A	90.9125	1839	2203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.75	96.24	0.87	0.84	8	-
GCF_900111895.1	s__Pseudomonas_E simiae	90.841	1728	2203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.45	99.32	0.95	0.92	20	-
GCF_001186335.1	s__Pseudomonas_E trivialis_B	90.2156	1768	2203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.34	95.31	0.86	0.86	8	-
GCF_002843605.1	s__Pseudomonas_E sp002843605	89.3011	1770	2203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.70	97.45	0.92	0.91	7	-
GCF_013386585.1	s__Pseudomonas_E sp013386585	89.1111	1691	2203	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_001050345.1	s__Pseudomonas_E fildesensis	88.8082	1620	2203	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:37:23,203] [INFO] GTDB search result was written to GCF_024112395.1_ASM2411239v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:37:23,204] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:37:23,208] [INFO] DFAST_QC result json was written to GCF_024112395.1_ASM2411239v1_genomic.fna/dqc_result.json
[2024-01-24 11:37:23,208] [INFO] DFAST_QC completed!
[2024-01-24 11:37:23,208] [INFO] Total running time: 0h2m30s