[2024-01-24 14:13:18,446] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:13:18,449] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:13:18,449] [INFO] DQC Reference Directory: /var/lib/cwl/stgbeb16e13-f23a-44fa-a95d-b80e6b71c91c/dqc_reference
[2024-01-24 14:13:19,762] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:13:19,763] [INFO] Task started: Prodigal
[2024-01-24 14:13:19,763] [INFO] Running command: gunzip -c /var/lib/cwl/stgb152d8de-5265-4aa2-b07d-e3104c29e817/GCF_004363035.1_ASM436303v1_genomic.fna.gz | prodigal -d GCF_004363035.1_ASM436303v1_genomic.fna/cds.fna -a GCF_004363035.1_ASM436303v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:13:29,332] [INFO] Task succeeded: Prodigal
[2024-01-24 14:13:29,332] [INFO] Task started: HMMsearch
[2024-01-24 14:13:29,332] [INFO] Running command: hmmsearch --tblout GCF_004363035.1_ASM436303v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbeb16e13-f23a-44fa-a95d-b80e6b71c91c/dqc_reference/reference_markers.hmm GCF_004363035.1_ASM436303v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:13:29,605] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:13:29,607] [INFO] Found 6/6 markers.
[2024-01-24 14:13:29,640] [INFO] Query marker FASTA was written to GCF_004363035.1_ASM436303v1_genomic.fna/markers.fasta
[2024-01-24 14:13:29,640] [INFO] Task started: Blastn
[2024-01-24 14:13:29,640] [INFO] Running command: blastn -query GCF_004363035.1_ASM436303v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbeb16e13-f23a-44fa-a95d-b80e6b71c91c/dqc_reference/reference_markers.fasta -out GCF_004363035.1_ASM436303v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:30,671] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:30,675] [INFO] Selected 23 target genomes.
[2024-01-24 14:13:30,676] [INFO] Target genome list was writen to GCF_004363035.1_ASM436303v1_genomic.fna/target_genomes.txt
[2024-01-24 14:13:30,691] [INFO] Task started: fastANI
[2024-01-24 14:13:30,692] [INFO] Running command: fastANI --query /var/lib/cwl/stgb152d8de-5265-4aa2-b07d-e3104c29e817/GCF_004363035.1_ASM436303v1_genomic.fna.gz --refList GCF_004363035.1_ASM436303v1_genomic.fna/target_genomes.txt --output GCF_004363035.1_ASM436303v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:48,124] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:48,124] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbeb16e13-f23a-44fa-a95d-b80e6b71c91c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:48,125] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbeb16e13-f23a-44fa-a95d-b80e6b71c91c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:48,142] [INFO] Found 23 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:13:48,142] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:13:48,142] [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
Thiopseudomonas denitrificans	strain=DSM 28679	GCA_004363035.1	1501432	1501432	type	True	100.0	931	931	95	conclusive
Thiopseudomonas denitrificans	strain=X2	GCA_002866065.1	1501432	1501432	type	True	99.9758	923	931	95	conclusive
Pseudomonas sagittaria	strain=JCM 18195	GCA_900115715.1	1135990	1135990	type	True	78.9008	300	931	95	below_threshold
Pseudomonas flexibilis	strain=ATCC 29606	GCA_000802425.1	706570	706570	type	True	78.8453	306	931	95	below_threshold
Pseudomonas flexibilis	strain=ATCC 29606	GCA_900155995.1	706570	706570	type	True	78.8427	308	931	95	below_threshold
Pseudomonas oryzae	strain=KCTC 32247	GCA_900104805.1	1392877	1392877	type	True	78.8254	310	931	95	below_threshold
Pseudomonas linyingensis	strain=LMG 25967	GCA_900109175.1	915471	915471	type	True	78.8058	310	931	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	78.7607	309	931	95	below_threshold
Pseudomonas delhiensis	strain=CCM 7361	GCA_900099945.1	366289	366289	type	True	78.7199	314	931	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	78.7096	311	931	95	below_threshold
Pseudomonas carbonaria	strain=CIP 111764	GCA_904061905.1	2762745	2762745	type	True	78.4296	321	931	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	78.4228	320	931	95	below_threshold
Pseudomonas campi	strain=S1-A32-2	GCA_013200955.2	2731681	2731681	type	True	78.3088	306	931	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	78.2872	285	931	95	below_threshold
Stutzerimonas azotifigens	strain=DSM 17556	GCA_000425625.1	291995	291995	type	True	78.2698	299	931	95	below_threshold
Pseudomonas argentinensis	strain=CCUG 50743	GCA_008801645.1	289370	289370	type	True	78.2362	294	931	95	below_threshold
Pseudomonas mangiferae	strain=DMKU BBB3-04	GCA_007109405.1	2593654	2593654	type	True	78.212	261	931	95	below_threshold
Pseudomonas thermotolerans	strain=DSM 14292	GCA_000364625.1	157784	157784	type	True	78.1503	293	931	95	below_threshold
Pseudomonas argentinensis	strain=LMG 22563	GCA_900113905.1	289370	289370	type	True	78.1288	293	931	95	below_threshold
Pseudomonas saudiphocaensis	strain=20_BN	GCA_000756775.2	1499686	1499686	type	True	78.0558	271	931	95	below_threshold
Pseudomonas punonensis	strain=CECT 8089	GCA_900142655.1	1220495	1220495	type	True	78.0453	240	931	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	77.9533	247	931	95	below_threshold
Pseudomonas kairouanensis	strain=KC12	GCA_004682055.1	2293832	2293832	type	True	77.4607	229	931	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:48,144] [INFO] DFAST Taxonomy check result was written to GCF_004363035.1_ASM436303v1_genomic.fna/tc_result.tsv
[2024-01-24 14:13:48,145] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:48,145] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:48,145] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbeb16e13-f23a-44fa-a95d-b80e6b71c91c/dqc_reference/checkm_data
[2024-01-24 14:13:48,146] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:48,179] [INFO] Task started: CheckM
[2024-01-24 14:13:48,179] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004363035.1_ASM436303v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004363035.1_ASM436303v1_genomic.fna/checkm_input GCF_004363035.1_ASM436303v1_genomic.fna/checkm_result
[2024-01-24 14:14:19,759] [INFO] Task succeeded: CheckM
[2024-01-24 14:14:19,761] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:14:19,783] [INFO] ===== Completeness check finished =====
[2024-01-24 14:14:19,783] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:14:19,784] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004363035.1_ASM436303v1_genomic.fna/markers.fasta)
[2024-01-24 14:14:19,784] [INFO] Task started: Blastn
[2024-01-24 14:14:19,784] [INFO] Running command: blastn -query GCF_004363035.1_ASM436303v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbeb16e13-f23a-44fa-a95d-b80e6b71c91c/dqc_reference/reference_markers_gtdb.fasta -out GCF_004363035.1_ASM436303v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:21,309] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:21,313] [INFO] Selected 20 target genomes.
[2024-01-24 14:14:21,313] [INFO] Target genome list was writen to GCF_004363035.1_ASM436303v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:14:21,331] [INFO] Task started: fastANI
[2024-01-24 14:14:21,331] [INFO] Running command: fastANI --query /var/lib/cwl/stgb152d8de-5265-4aa2-b07d-e3104c29e817/GCF_004363035.1_ASM436303v1_genomic.fna.gz --refList GCF_004363035.1_ASM436303v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004363035.1_ASM436303v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:14:36,857] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:36,878] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:14:36,878] [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_002866065.1	s__Thiopseudomonas denitrificans	99.9758	923	931	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Thiopseudomonas	95.0	99.98	99.98	0.99	0.99	2	conclusive
GCA_012728415.1	s__Thiopseudomonas sp012728415	82.0276	565	931	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Thiopseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018384595.1	s__Thiopseudomonas sp018384595	81.0019	469	931	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Thiopseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109175.1	s__Pseudomonas_K linyingensis	78.792	311	931	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019097855.1	s__Pseudomonas_K sp019097855	78.6742	313	931	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009799925.1	s__Pseudomonas_E sp009799925	78.6725	324	931	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_002304225.1	s__Pseudomonas_E sp002304225	78.6084	280	931	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.09	95.09	0.93	0.93	2	-
GCF_014490745.1	s__Pseudomonas_E alcaligenes_C	78.5429	325	931	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_005508865.1	s__Pseudomonas_E sp005508865	78.5331	313	931	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_001592875.1	s__Pseudomonas_E sp001592875	78.5297	291	931	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_001839655.1	s__Pseudomonas_E argentinensis_B	78.4758	285	931	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_904061905.1	s__Pseudomonas_E carbonaria	78.4343	319	931	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_015070855.1	s__Pseudomonas_A lopnurensis	78.3477	330	931	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_000425625.1	s__Pseudomonas_N azotifigens	78.2829	298	931	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_N	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013522825.1	s__Pseudomonas_A stutzeri_AK	78.2413	303	931	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_000364625.1	s__Pseudomonas_E thermotolerans	78.1746	290	931	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.25	99.24	0.93	0.93	3	-
GCF_000282535.1	s__Pseudomonas_E sp000282535	78.1421	253	931	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_900113905.1	s__Pseudomonas_E argentinensis	78.1173	294	931	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_001547895.1	s__Pseudomonas_E sp001547895	78.0205	261	931	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.12	98.88	0.95	0.94	4	-
GCF_902506535.1	s__Pseudomonas_E sp902506535	77.9876	254	931	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 14:14:36,880] [INFO] GTDB search result was written to GCF_004363035.1_ASM436303v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:14:36,880] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:14:36,885] [INFO] DFAST_QC result json was written to GCF_004363035.1_ASM436303v1_genomic.fna/dqc_result.json
[2024-01-24 14:14:36,885] [INFO] DFAST_QC completed!
[2024-01-24 14:14:36,885] [INFO] Total running time: 0h1m18s