[2024-01-24 12:53:57,154] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:57,163] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:57,164] [INFO] DQC Reference Directory: /var/lib/cwl/stgba1da36d-940f-4c41-9cb1-cbed5b7bf40f/dqc_reference
[2024-01-24 12:53:58,507] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:58,508] [INFO] Task started: Prodigal
[2024-01-24 12:53:58,509] [INFO] Running command: gunzip -c /var/lib/cwl/stg865126fa-fa77-4c1b-97df-5bee471a4ccf/GCF_004327335.1_ASM432733v1_genomic.fna.gz | prodigal -d GCF_004327335.1_ASM432733v1_genomic.fna/cds.fna -a GCF_004327335.1_ASM432733v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:13,762] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:13,762] [INFO] Task started: HMMsearch
[2024-01-24 12:54:13,762] [INFO] Running command: hmmsearch --tblout GCF_004327335.1_ASM432733v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgba1da36d-940f-4c41-9cb1-cbed5b7bf40f/dqc_reference/reference_markers.hmm GCF_004327335.1_ASM432733v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:14,014] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:14,016] [INFO] Found 6/6 markers.
[2024-01-24 12:54:14,052] [INFO] Query marker FASTA was written to GCF_004327335.1_ASM432733v1_genomic.fna/markers.fasta
[2024-01-24 12:54:14,052] [INFO] Task started: Blastn
[2024-01-24 12:54:14,053] [INFO] Running command: blastn -query GCF_004327335.1_ASM432733v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba1da36d-940f-4c41-9cb1-cbed5b7bf40f/dqc_reference/reference_markers.fasta -out GCF_004327335.1_ASM432733v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:15,047] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:15,051] [INFO] Selected 26 target genomes.
[2024-01-24 12:54:15,051] [INFO] Target genome list was writen to GCF_004327335.1_ASM432733v1_genomic.fna/target_genomes.txt
[2024-01-24 12:54:15,058] [INFO] Task started: fastANI
[2024-01-24 12:54:15,058] [INFO] Running command: fastANI --query /var/lib/cwl/stg865126fa-fa77-4c1b-97df-5bee471a4ccf/GCF_004327335.1_ASM432733v1_genomic.fna.gz --refList GCF_004327335.1_ASM432733v1_genomic.fna/target_genomes.txt --output GCF_004327335.1_ASM432733v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:37,712] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:37,713] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgba1da36d-940f-4c41-9cb1-cbed5b7bf40f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:37,713] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgba1da36d-940f-4c41-9cb1-cbed5b7bf40f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:37,735] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:54:37,735] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:54:37,735] [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 nitrititolerans	strain=GL14	GCA_003696285.1	2482751	2482751	type	True	81.4756	616	1412	95	below_threshold
Stutzerimonas azotifigens	strain=DSM 17556	GCA_000425625.1	291995	291995	type	True	81.4646	640	1412	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	81.3142	575	1412	95	below_threshold
Pseudomonas benzenivorans	strain=DSM 8628	GCA_900100495.1	556533	556533	type	True	81.2503	661	1412	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	81.1956	636	1412	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_002891015.1	2968968	2968968	type	True	81.1278	618	1412	95	below_threshold
Stutzerimonas stutzeri	strain=CGMCC 1.1803	GCA_000219605.1	316	316	type	True	81.0829	628	1412	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	81.077	623	1412	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	81.0565	609	1412	95	below_threshold
Stutzerimonas stutzeri	strain=FDAARGOS_875	GCA_016028655.1	316	316	type	True	81.0333	638	1412	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_024448335.1	2968969	2968969	type	True	81.0084	602	1412	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	80.9143	613	1412	95	below_threshold
Azotobacter beijerinckii	strain=DSM 378	GCA_900110885.1	170623	170623	type	True	80.9011	561	1412	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	80.8635	595	1412	95	below_threshold
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	80.847	621	1412	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	80.838	589	1412	95	below_threshold
Pseudomonas flexibilis	strain=ATCC 29606	GCA_000802425.1	706570	706570	type	True	80.8031	540	1412	95	below_threshold
Pseudomonas flexibilis	strain=ATCC 29606	GCA_900155995.1	706570	706570	type	True	80.7905	536	1412	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_024397575.1	1211807	1211807	type	True	80.7704	583	1412	95	below_threshold
Pseudomonas aeruginosa	strain=CCUG 551	GCA_008801675.1	287	287	type	True	80.7295	655	1412	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_012987025.1	287	287	type	True	80.7039	654	1412	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_900114065.1	1211807	1211807	type	True	80.7027	598	1412	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	80.6805	663	1412	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	80.645	676	1412	95	below_threshold
Pseudomonas otitidis	strain=DSM 17224	GCA_900111835.1	319939	319939	suspected-type	True	80.6055	667	1412	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_900167195.1	287	287	type	True	80.6042	662	1412	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:37,738] [INFO] DFAST Taxonomy check result was written to GCF_004327335.1_ASM432733v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:37,739] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:37,739] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:37,739] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgba1da36d-940f-4c41-9cb1-cbed5b7bf40f/dqc_reference/checkm_data
[2024-01-24 12:54:37,740] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:37,784] [INFO] Task started: CheckM
[2024-01-24 12:54:37,784] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004327335.1_ASM432733v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004327335.1_ASM432733v1_genomic.fna/checkm_input GCF_004327335.1_ASM432733v1_genomic.fna/checkm_result
[2024-01-24 12:55:19,855] [INFO] Task succeeded: CheckM
[2024-01-24 12:55:19,856] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:55:19,875] [INFO] ===== Completeness check finished =====
[2024-01-24 12:55:19,875] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:55:19,876] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004327335.1_ASM432733v1_genomic.fna/markers.fasta)
[2024-01-24 12:55:19,876] [INFO] Task started: Blastn
[2024-01-24 12:55:19,876] [INFO] Running command: blastn -query GCF_004327335.1_ASM432733v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba1da36d-940f-4c41-9cb1-cbed5b7bf40f/dqc_reference/reference_markers_gtdb.fasta -out GCF_004327335.1_ASM432733v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:55:21,854] [INFO] Task succeeded: Blastn
[2024-01-24 12:55:21,858] [INFO] Selected 15 target genomes.
[2024-01-24 12:55:21,858] [INFO] Target genome list was writen to GCF_004327335.1_ASM432733v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:55:21,865] [INFO] Task started: fastANI
[2024-01-24 12:55:21,865] [INFO] Running command: fastANI --query /var/lib/cwl/stg865126fa-fa77-4c1b-97df-5bee471a4ccf/GCF_004327335.1_ASM432733v1_genomic.fna.gz --refList GCF_004327335.1_ASM432733v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004327335.1_ASM432733v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:55:36,581] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:36,595] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:55:36,595] [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_004327335.1	s__Pseudomonas_Q kirkiae	100.0	1409	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_Q	95.0	99.65	99.41	0.96	0.94	4	conclusive
GCF_013395055.1	s__Pseudomonas_Q sp013395055	87.1662	968	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_Q	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002890915.1	s__Pseudomonas_A stutzeri_AF	82.1401	709	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.35	98.08	0.91	0.89	3	-
GCF_015070855.1	s__Pseudomonas_A lopnurensis	82.1132	726	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.76	98.41	0.83	0.83	4	-
GCF_904061905.1	s__Pseudomonas_E carbonaria	81.7208	684	1412	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_000263395.1	s__Pseudomonas_A stutzeri_C	81.623	621	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003696285.1	s__Pseudomonas_A nitrititolerans	81.4486	617	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.45	96.83	0.90	0.83	53	-
GCF_004801855.1	s__Pseudomonas_K sp004801855	81.4055	561	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	98.38	98.38	0.89	0.89	2	-
GCA_002483005.1	s__Pseudomonas_E sp002483005	81.2079	400	1412	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_018398425.1	s__Pseudomonas_E lalucatii	81.195	636	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.68	99.28	0.97	0.92	4	-
GCF_003205815.1	s__Pseudomonas_A sp003205815	81.0067	628	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.18	96.58	0.91	0.87	27	-
GCF_900110885.1	s__Azotobacter beijerinckii	80.891	562	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Azotobacter	95.0	97.34	96.47	0.86	0.85	5	-
GCF_000017205.1	s__Pseudomonas aeruginosa_A	80.8114	679	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	99.07	98.78	0.93	0.80	42	-
GCF_000474255.1	s__Pseudomonas_F alcaligenes_A	80.4804	701	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	98.08	97.69	0.89	0.89	3	-
GCA_900766265.1	s__Pseudomonas_R sp900766265	80.4174	555	1412	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_R	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:55:36,596] [INFO] GTDB search result was written to GCF_004327335.1_ASM432733v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:55:36,597] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:55:36,602] [INFO] DFAST_QC result json was written to GCF_004327335.1_ASM432733v1_genomic.fna/dqc_result.json
[2024-01-24 12:55:36,602] [INFO] DFAST_QC completed!
[2024-01-24 12:55:36,602] [INFO] Total running time: 0h1m39s