[2023-06-28 23:25:16,323] [INFO] DFAST_QC pipeline started.
[2023-06-28 23:25:16,326] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 23:25:16,326] [INFO] DQC Reference Directory: /var/lib/cwl/stg5fc25e24-acd3-42f5-8e1c-8325688e2cb5/dqc_reference
[2023-06-28 23:25:17,582] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 23:25:17,583] [INFO] Task started: Prodigal
[2023-06-28 23:25:17,583] [INFO] Running command: gunzip -c /var/lib/cwl/stg9fc0c10a-b3e6-44e5-8646-b06304c4914f/GCA_027310225.1_ASM2731022v1_genomic.fna.gz | prodigal -d GCA_027310225.1_ASM2731022v1_genomic.fna/cds.fna -a GCA_027310225.1_ASM2731022v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 23:25:25,997] [INFO] Task succeeded: Prodigal
[2023-06-28 23:25:25,998] [INFO] Task started: HMMsearch
[2023-06-28 23:25:25,998] [INFO] Running command: hmmsearch --tblout GCA_027310225.1_ASM2731022v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5fc25e24-acd3-42f5-8e1c-8325688e2cb5/dqc_reference/reference_markers.hmm GCA_027310225.1_ASM2731022v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 23:25:26,246] [INFO] Task succeeded: HMMsearch
[2023-06-28 23:25:26,247] [INFO] Found 6/6 markers.
[2023-06-28 23:25:26,277] [INFO] Query marker FASTA was written to GCA_027310225.1_ASM2731022v1_genomic.fna/markers.fasta
[2023-06-28 23:25:26,278] [INFO] Task started: Blastn
[2023-06-28 23:25:26,278] [INFO] Running command: blastn -query GCA_027310225.1_ASM2731022v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5fc25e24-acd3-42f5-8e1c-8325688e2cb5/dqc_reference/reference_markers.fasta -out GCA_027310225.1_ASM2731022v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:25:27,177] [INFO] Task succeeded: Blastn
[2023-06-28 23:25:27,182] [INFO] Selected 23 target genomes.
[2023-06-28 23:25:27,182] [INFO] Target genome list was writen to GCA_027310225.1_ASM2731022v1_genomic.fna/target_genomes.txt
[2023-06-28 23:25:27,184] [INFO] Task started: fastANI
[2023-06-28 23:25:27,184] [INFO] Running command: fastANI --query /var/lib/cwl/stg9fc0c10a-b3e6-44e5-8646-b06304c4914f/GCA_027310225.1_ASM2731022v1_genomic.fna.gz --refList GCA_027310225.1_ASM2731022v1_genomic.fna/target_genomes.txt --output GCA_027310225.1_ASM2731022v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 23:25:42,655] [INFO] Task succeeded: fastANI
[2023-06-28 23:25:42,655] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5fc25e24-acd3-42f5-8e1c-8325688e2cb5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 23:25:42,655] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5fc25e24-acd3-42f5-8e1c-8325688e2cb5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 23:25:42,671] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 23:25:42,671] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 23:25:42,671] [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
Pelomicrobium methylotrophicum	strain=SM250	GCA_008014345.1	2602750	2602750	type	True	77.0826	139	905	95	below_threshold
Sulfuritortus calidifontis	strain=J1A	GCA_003967275.1	1914471	1914471	type	True	76.9924	131	905	95	below_threshold
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	76.9663	173	905	95	below_threshold
Sulfuritortus calidifontis	strain=DSM 103923	GCA_004346085.1	1914471	1914471	type	True	76.9002	129	905	95	below_threshold
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	76.791	192	905	95	below_threshold
Crenobacter luteus	strain=DSM 27258	GCA_004345725.1	1452487	1452487	type	True	76.7057	150	905	95	below_threshold
Ferrigenium kumadai	strain=An22	GCA_018324385.1	1682490	1682490	type	True	76.6043	95	905	95	below_threshold
Thauera chlorobenzoica	strain=3CB-1	GCA_900108255.1	96773	96773	type	True	76.5382	155	905	95	below_threshold
Azoarcus rhizosphaerae	strain=CC-YHH848	GCA_004801305.1	2565932	2565932	type	True	76.4517	173	905	95	below_threshold
Methyloversatilis discipulorum	strain=FAM1	GCA_000527135.1	1119528	1119528	type	True	76.399	155	905	95	below_threshold
Sulfurimicrobium lacus	strain=skT11	GCA_011764585.1	2715678	2715678	type	True	76.3476	100	905	95	below_threshold
Nitrogeniibacter mangrovi	strain=M9-3-2	GCA_010983895.1	2016596	2016596	type	True	76.2914	129	905	95	below_threshold
Vogesella alkaliphila	strain=KCTC 32041	GCA_014652475.1	1193621	1193621	type	True	76.2874	115	905	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	76.1192	132	905	95	below_threshold
Thioalkalivibrio thiocyanodenitrificans	strain=ARhD 1	GCA_000378965.1	243063	243063	type	True	76.0566	59	905	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	76.0517	132	905	95	below_threshold
Vogesella fluminis	strain=KCTC 23713	GCA_014652335.1	1069161	1069161	type	True	76.0059	97	905	95	below_threshold
Vogesella urethralis	strain=YM-1	GCA_007644045.2	2592656	2592656	type	True	75.9379	69	905	95	below_threshold
Vogesella indigofera	strain=DSM 3303	GCA_003633895.1	45465	45465	type	True	75.8611	94	905	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 23:25:42,673] [INFO] DFAST Taxonomy check result was written to GCA_027310225.1_ASM2731022v1_genomic.fna/tc_result.tsv
[2023-06-28 23:25:42,674] [INFO] ===== Taxonomy check completed =====
[2023-06-28 23:25:42,674] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 23:25:42,674] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5fc25e24-acd3-42f5-8e1c-8325688e2cb5/dqc_reference/checkm_data
[2023-06-28 23:25:42,675] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 23:25:42,712] [INFO] Task started: CheckM
[2023-06-28 23:25:42,712] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027310225.1_ASM2731022v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027310225.1_ASM2731022v1_genomic.fna/checkm_input GCA_027310225.1_ASM2731022v1_genomic.fna/checkm_result
[2023-06-28 23:26:13,426] [INFO] Task succeeded: CheckM
[2023-06-28 23:26:13,428] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.85%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 23:26:13,450] [INFO] ===== Completeness check finished =====
[2023-06-28 23:26:13,451] [INFO] ===== Start GTDB Search =====
[2023-06-28 23:26:13,452] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027310225.1_ASM2731022v1_genomic.fna/markers.fasta)
[2023-06-28 23:26:13,452] [INFO] Task started: Blastn
[2023-06-28 23:26:13,453] [INFO] Running command: blastn -query GCA_027310225.1_ASM2731022v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5fc25e24-acd3-42f5-8e1c-8325688e2cb5/dqc_reference/reference_markers_gtdb.fasta -out GCA_027310225.1_ASM2731022v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:26:14,846] [INFO] Task succeeded: Blastn
[2023-06-28 23:26:14,851] [INFO] Selected 15 target genomes.
[2023-06-28 23:26:14,851] [INFO] Target genome list was writen to GCA_027310225.1_ASM2731022v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 23:26:14,860] [INFO] Task started: fastANI
[2023-06-28 23:26:14,861] [INFO] Running command: fastANI --query /var/lib/cwl/stg9fc0c10a-b3e6-44e5-8646-b06304c4914f/GCA_027310225.1_ASM2731022v1_genomic.fna.gz --refList GCA_027310225.1_ASM2731022v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027310225.1_ASM2731022v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 23:26:25,166] [INFO] Task succeeded: fastANI
[2023-06-28 23:26:25,184] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 23:26:25,185] [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
GCA_016177355.1	s__SG8-41 sp016177355	81.5382	306	905	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-41;g__SG8-41	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011330925.1	s__SG8-41 sp011330925	81.3425	318	905	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-41;g__SG8-41	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016183675.1	s__SG8-41 sp016183675	81.0016	469	905	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-41;g__SG8-41	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016192825.1	s__SG8-41 sp016192825	80.8616	529	905	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-41;g__SG8-41	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001771935.1	s__SG8-41 sp001771935	80.8201	477	905	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-41;g__SG8-41	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016868035.1	s__SG8-41 sp016868035	79.4493	465	905	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-41;g__SG8-41	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001772005.1	s__DSOT01 sp001772005	78.8634	430	905	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-41;g__DSOT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011046905.1	s__DSOT01 sp011046905	78.7981	395	905	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-41;g__DSOT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001771985.1	s__DSOT01 sp001771985	78.5322	352	905	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-41;g__DSOT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016202565.1	s__DSOT01 sp016202565	78.1638	341	905	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-41;g__DSOT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001953215.1	s__Usitatibacter sp001953215	76.7	166	905	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Usitatibacteraceae;g__Usitatibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019136105.1	s__RPQJ01 sp019136105	76.2815	65	905	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__RPQJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005889025.1	s__PALSA-1003 sp005889025	75.8647	71	905	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Casimicrobiaceae;g__PALSA-1003	95.0	98.27	98.27	0.83	0.83	2	-
GCA_002995625.1	s__UDEA-SF1 sp002995625	75.7556	91	905	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Ahniellaceae;g__UDEA-SF1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 23:26:25,187] [INFO] GTDB search result was written to GCA_027310225.1_ASM2731022v1_genomic.fna/result_gtdb.tsv
[2023-06-28 23:26:25,188] [INFO] ===== GTDB Search completed =====
[2023-06-28 23:26:25,196] [INFO] DFAST_QC result json was written to GCA_027310225.1_ASM2731022v1_genomic.fna/dqc_result.json
[2023-06-28 23:26:25,196] [INFO] DFAST_QC completed!
[2023-06-28 23:26:25,196] [INFO] Total running time: 0h1m9s