[2024-01-24 12:13:23,552] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:23,557] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:23,557] [INFO] DQC Reference Directory: /var/lib/cwl/stg876cf1b4-a76d-43de-b723-b3932c59671a/dqc_reference
[2024-01-24 12:13:26,492] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:26,493] [INFO] Task started: Prodigal
[2024-01-24 12:13:26,495] [INFO] Running command: gunzip -c /var/lib/cwl/stg7ada93ff-d057-412f-a32d-031820638785/GCF_001730655.1_ASM173065v1_genomic.fna.gz | prodigal -d GCF_001730655.1_ASM173065v1_genomic.fna/cds.fna -a GCF_001730655.1_ASM173065v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:48,094] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:48,095] [INFO] Task started: HMMsearch
[2024-01-24 12:13:48,095] [INFO] Running command: hmmsearch --tblout GCF_001730655.1_ASM173065v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg876cf1b4-a76d-43de-b723-b3932c59671a/dqc_reference/reference_markers.hmm GCF_001730655.1_ASM173065v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:48,465] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:48,467] [INFO] Found 6/6 markers.
[2024-01-24 12:13:48,525] [INFO] Query marker FASTA was written to GCF_001730655.1_ASM173065v1_genomic.fna/markers.fasta
[2024-01-24 12:13:48,526] [INFO] Task started: Blastn
[2024-01-24 12:13:48,526] [INFO] Running command: blastn -query GCF_001730655.1_ASM173065v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg876cf1b4-a76d-43de-b723-b3932c59671a/dqc_reference/reference_markers.fasta -out GCF_001730655.1_ASM173065v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:49,500] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:49,504] [INFO] Selected 15 target genomes.
[2024-01-24 12:13:49,505] [INFO] Target genome list was writen to GCF_001730655.1_ASM173065v1_genomic.fna/target_genomes.txt
[2024-01-24 12:13:49,511] [INFO] Task started: fastANI
[2024-01-24 12:13:49,512] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ada93ff-d057-412f-a32d-031820638785/GCF_001730655.1_ASM173065v1_genomic.fna.gz --refList GCF_001730655.1_ASM173065v1_genomic.fna/target_genomes.txt --output GCF_001730655.1_ASM173065v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:13,857] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:13,858] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg876cf1b4-a76d-43de-b723-b3932c59671a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:13,858] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg876cf1b4-a76d-43de-b723-b3932c59671a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:13,872] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:14:13,872] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:13,873] [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 trivialis	strain=LMG 21464	GCA_001730655.1	200450	200450	type	True	100.0	1871	1895	95	conclusive
Pseudomonas trivialis	strain=DSM 14937	GCA_001439805.1	200450	200450	type	True	99.9893	1828	1895	95	conclusive
Pseudomonas poae	strain=DSM 14936	GCA_001439785.1	200451	200451	type	True	93.7635	1629	1895	95	below_threshold
Pseudomonas poae	strain=LMG 21465	GCA_001730605.1	200451	200451	type	True	93.7497	1641	1895	95	below_threshold
Pseudomonas marginalis	strain=DSM 13124	GCA_007858155.1	298	298	suspected-type	True	87.9322	1398	1895	95	below_threshold
Pseudomonas azotoformans	strain=NBRC 12693	GCA_002091515.1	47878	47878	suspected-type	True	87.8359	1402	1895	95	below_threshold
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	87.6905	1432	1895	95	below_threshold
Pseudomonas salomonii	strain=ICMP 14252	GCA_900107155.1	191391	191391	type	True	87.4605	1422	1895	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	87.4358	1405	1895	95	below_threshold
Pseudomonas cedrina subsp. cedrina		GCA_900625035.1	76762	651740	type	True	87.4095	1409	1895	95	below_threshold
Pseudomonas canadensis	strain=2-92	GCA_000503215.1	915099	915099	type	True	87.4044	1391	1895	95	below_threshold
Pseudomonas extremaustralis	strain=DSM 17835	GCA_007858235.1	359110	359110	type	True	87.3844	1307	1895	95	below_threshold
Pseudomonas spelaei	strain=CCM 7893	GCA_009724245.1	1055469	1055469	type	True	85.4399	1257	1895	95	below_threshold
Pseudomonas karstica	strain=CCM 7891	GCA_009707515.1	1055468	1055468	type	True	84.6399	1193	1895	95	below_threshold
Nakamurella aerolata	strain=DB0629	GCA_013002705.1	1656892	1656892	type	True	75.002	78	1895	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:13,874] [INFO] DFAST Taxonomy check result was written to GCF_001730655.1_ASM173065v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:13,875] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:13,875] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:13,875] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg876cf1b4-a76d-43de-b723-b3932c59671a/dqc_reference/checkm_data
[2024-01-24 12:14:13,876] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:13,937] [INFO] Task started: CheckM
[2024-01-24 12:14:13,937] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001730655.1_ASM173065v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001730655.1_ASM173065v1_genomic.fna/checkm_input GCF_001730655.1_ASM173065v1_genomic.fna/checkm_result
[2024-01-24 12:15:20,994] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:20,995] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:21,024] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:21,025] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:21,025] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001730655.1_ASM173065v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:21,026] [INFO] Task started: Blastn
[2024-01-24 12:15:21,026] [INFO] Running command: blastn -query GCF_001730655.1_ASM173065v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg876cf1b4-a76d-43de-b723-b3932c59671a/dqc_reference/reference_markers_gtdb.fasta -out GCF_001730655.1_ASM173065v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:22,666] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:22,670] [INFO] Selected 25 target genomes.
[2024-01-24 12:15:22,670] [INFO] Target genome list was writen to GCF_001730655.1_ASM173065v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:22,685] [INFO] Task started: fastANI
[2024-01-24 12:15:22,685] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ada93ff-d057-412f-a32d-031820638785/GCF_001730655.1_ASM173065v1_genomic.fna.gz --refList GCF_001730655.1_ASM173065v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001730655.1_ASM173065v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:00,962] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:00,983] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:00,984] [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_001439805.1	s__Pseudomonas_E trivialis	99.9893	1828	1895	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.47	95.41	0.96	0.87	4	conclusive
GCF_001439785.1	s__Pseudomonas_E poae	93.7517	1630	1895	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.09	98.80	0.95	0.92	10	-
GCF_003097075.1	s__Pseudomonas_E sp003097075	88.3099	1394	1895	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.77	98.77	0.94	0.94	2	-
GCF_900580675.1	s__Pseudomonas_E sp900580675	87.9433	1340	1895	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_900103345.1	s__Pseudomonas_E azotoformans	87.9155	1408	1895	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_002843605.1	s__Pseudomonas_E sp002843605	87.8851	1427	1895	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_001269925.1	s__Pseudomonas_E sp001269925	87.7844	1454	1895	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_000346755.1	s__Pseudomonas_E sp000346755	87.7802	1340	1895	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_001439815.1	s__Pseudomonas_E orientalis	87.6134	1406	1895	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.01	96.05	0.91	0.89	6	-
GCF_002022265.1	s__Pseudomonas_E fluorescens_C	87.6003	1409	1895	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.28	96.98	0.88	0.86	8	-
GCF_009834565.1	s__Pseudomonas_E sp009834565	87.5658	1437	1895	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.71	97.35	0.93	0.93	3	-
GCF_001645105.1	s__Pseudomonas_E marginalis_B	87.5435	1411	1895	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_001579805.1	s__Pseudomonas_E azotoformans_A	87.541	1413	1895	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_012844475.1	s__Pseudomonas_E sp012844475	87.4919	1326	1895	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900102035.1	s__Pseudomonas_E extremaustralis	87.4872	1347	1895	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.74	98.99	0.98	0.92	5	-
GCF_001983175.1	s__Pseudomonas_E cedrina	87.4616	1403	1895	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.10	97.30	0.97	0.92	4	-
GCF_900107155.1	s__Pseudomonas_E salomonii	87.461	1423	1895	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.30	96.43	0.92	0.87	14	-
GCF_002563895.1	s__Pseudomonas_E lurida	87.4432	1404	1895	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_001708445.1	s__Pseudomonas_E fluorescens_AN	87.439	1416	1895	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.17	98.56	0.90	0.82	34	-
GCF_000503215.1	s__Pseudomonas_E canadensis	87.4084	1389	1895	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_013385965.1	s__Pseudomonas_E edaphica	87.2343	1408	1895	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.04	98.93	0.94	0.92	9	-
GCF_001647715.1	s__Pseudomonas_E antarctica_A	87.1676	1405	1895	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.45	97.45	0.91	0.91	2	-
GCF_009659625.1	s__Pseudomonas_E haemolytica	87.1607	1367	1895	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.47	98.83	0.97	0.95	8	-
GCF_001439735.1	s__Pseudomonas_E paralactis	87.0409	1384	1895	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.61	98.52	0.94	0.92	4	-
GCF_009707515.1	s__Pseudomonas_E sp009707515	84.6734	1189	1895	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 12:16:00,992] [INFO] GTDB search result was written to GCF_001730655.1_ASM173065v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:00,993] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:01,001] [INFO] DFAST_QC result json was written to GCF_001730655.1_ASM173065v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:01,001] [INFO] DFAST_QC completed!
[2024-01-24 12:16:01,001] [INFO] Total running time: 0h2m37s