[2024-01-24 13:58:25,299] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:25,301] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:25,301] [INFO] DQC Reference Directory: /var/lib/cwl/stg3b0909bd-f5a3-4220-bd02-ce5cbf0ee514/dqc_reference
[2024-01-24 13:58:26,636] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:26,637] [INFO] Task started: Prodigal
[2024-01-24 13:58:26,638] [INFO] Running command: gunzip -c /var/lib/cwl/stged94aa75-e445-49a3-8a2f-0641bf6938c4/GCF_000015865.1_ASM1586v1_genomic.fna.gz | prodigal -d GCF_000015865.1_ASM1586v1_genomic.fna/cds.fna -a GCF_000015865.1_ASM1586v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:36,046] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:36,046] [INFO] Task started: HMMsearch
[2024-01-24 13:58:36,046] [INFO] Running command: hmmsearch --tblout GCF_000015865.1_ASM1586v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3b0909bd-f5a3-4220-bd02-ce5cbf0ee514/dqc_reference/reference_markers.hmm GCF_000015865.1_ASM1586v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:36,364] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:36,366] [INFO] Found 6/6 markers.
[2024-01-24 13:58:36,400] [INFO] Query marker FASTA was written to GCF_000015865.1_ASM1586v1_genomic.fna/markers.fasta
[2024-01-24 13:58:36,400] [INFO] Task started: Blastn
[2024-01-24 13:58:36,400] [INFO] Running command: blastn -query GCF_000015865.1_ASM1586v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3b0909bd-f5a3-4220-bd02-ce5cbf0ee514/dqc_reference/reference_markers.fasta -out GCF_000015865.1_ASM1586v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:37,044] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:37,048] [INFO] Selected 11 target genomes.
[2024-01-24 13:58:37,048] [INFO] Target genome list was writen to GCF_000015865.1_ASM1586v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:37,054] [INFO] Task started: fastANI
[2024-01-24 13:58:37,054] [INFO] Running command: fastANI --query /var/lib/cwl/stged94aa75-e445-49a3-8a2f-0641bf6938c4/GCF_000015865.1_ASM1586v1_genomic.fna.gz --refList GCF_000015865.1_ASM1586v1_genomic.fna/target_genomes.txt --output GCF_000015865.1_ASM1586v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:46,642] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:46,642] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3b0909bd-f5a3-4220-bd02-ce5cbf0ee514/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:46,643] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3b0909bd-f5a3-4220-bd02-ce5cbf0ee514/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:46,650] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:46,651] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:46,651] [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
Acetivibrio thermocellus	strain=ATCC 27405	GCA_000015865.1	1515	1515	type	True	100.0	1281	1281	95	conclusive
Acetivibrio straminisolvens	strain=JCM 21531	GCA_000521465.1	253314	253314	type	True	84.3353	894	1281	95	below_threshold
Acetivibrio mesophilus	strain=N2K1	GCA_004102745.1	2487273	2487273	type	True	81.74	865	1281	95	below_threshold
Pseudoclostridium thermosuccinogenes	strain=DSM 5807	GCA_002896855.1	84032	84032	type	True	80.9712	92	1281	95	below_threshold
Acetivibrio saccincola	strain=GGR1	GCA_002844395.1	1677857	1677857	type	True	80.6208	140	1281	95	below_threshold
Acetivibrio cellulolyticus	strain=CD2	GCA_000179595.2	35830	35830	type	True	76.6311	101	1281	95	below_threshold
Anaerobacterium chartisolvens	strain=DSM 27016	GCA_003337415.1	1297424	1297424	type	True	76.2992	57	1281	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:46,652] [INFO] DFAST Taxonomy check result was written to GCF_000015865.1_ASM1586v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:46,653] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:46,653] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:46,653] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3b0909bd-f5a3-4220-bd02-ce5cbf0ee514/dqc_reference/checkm_data
[2024-01-24 13:58:46,654] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:46,701] [INFO] Task started: CheckM
[2024-01-24 13:58:46,701] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000015865.1_ASM1586v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000015865.1_ASM1586v1_genomic.fna/checkm_input GCF_000015865.1_ASM1586v1_genomic.fna/checkm_result
[2024-01-24 13:59:23,055] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:23,056] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:23,077] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:23,077] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:23,078] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000015865.1_ASM1586v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:23,078] [INFO] Task started: Blastn
[2024-01-24 13:59:23,079] [INFO] Running command: blastn -query GCF_000015865.1_ASM1586v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3b0909bd-f5a3-4220-bd02-ce5cbf0ee514/dqc_reference/reference_markers_gtdb.fasta -out GCF_000015865.1_ASM1586v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:24,150] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:24,153] [INFO] Selected 10 target genomes.
[2024-01-24 13:59:24,154] [INFO] Target genome list was writen to GCF_000015865.1_ASM1586v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:24,164] [INFO] Task started: fastANI
[2024-01-24 13:59:24,165] [INFO] Running command: fastANI --query /var/lib/cwl/stged94aa75-e445-49a3-8a2f-0641bf6938c4/GCF_000015865.1_ASM1586v1_genomic.fna.gz --refList GCF_000015865.1_ASM1586v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000015865.1_ASM1586v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:31,295] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:31,308] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:31,309] [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_000015865.1	s__Hungateiclostridium thermocellum	100.0	1281	1281	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__Acetivibrionaceae;g__Hungateiclostridium	95.0	99.61	99.46	0.95	0.92	14	conclusive
GCA_000521465.1	s__Hungateiclostridium straminisolvens	84.3539	891	1281	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__Acetivibrionaceae;g__Hungateiclostridium	95.0	99.73	99.73	0.92	0.92	2	-
GCF_004102745.1	s__Hungateiclostridium mesophilum	81.7343	865	1281	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__Acetivibrionaceae;g__Hungateiclostridium	95.0	99.61	99.52	0.93	0.90	4	-
GCF_002844395.1	s__Herbivorax saccincola	80.7636	140	1281	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__Acetivibrionaceae;g__Herbivorax	95.0	99.55	99.29	0.94	0.85	5	-
GCA_001512505.1	s__Hungateiclostridium sp001512505	78.4612	320	1281	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__Acetivibrionaceae;g__Hungateiclostridium	95.0	99.73	99.73	0.91	0.91	2	-
GCA_012523755.1	s__Hungateiclostridium sp012523755	77.2162	233	1281	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__Acetivibrionaceae;g__Hungateiclostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012840085.1	s__DUMB01 sp012840085	77.1906	68	1281	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__DUMB01;g__DUMB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012517995.1	s__Herbivorax sp012517995	76.3744	94	1281	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__Acetivibrionaceae;g__Herbivorax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:31,310] [INFO] GTDB search result was written to GCF_000015865.1_ASM1586v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:31,311] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:31,314] [INFO] DFAST_QC result json was written to GCF_000015865.1_ASM1586v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:31,314] [INFO] DFAST_QC completed!
[2024-01-24 13:59:31,314] [INFO] Total running time: 0h1m6s