[2024-01-24 13:48:42,493] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:42,496] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:42,496] [INFO] DQC Reference Directory: /var/lib/cwl/stgdd40743d-4280-4548-9dbb-cfc90e7193ca/dqc_reference
[2024-01-24 13:48:43,732] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:48:43,733] [INFO] Task started: Prodigal
[2024-01-24 13:48:43,733] [INFO] Running command: gunzip -c /var/lib/cwl/stg44f86e0d-98b9-43b5-b47d-7c045d6075bb/GCF_000179595.2_ASM17959v2_genomic.fna.gz | prodigal -d GCF_000179595.2_ASM17959v2_genomic.fna/cds.fna -a GCF_000179595.2_ASM17959v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:48:56,213] [INFO] Task succeeded: Prodigal
[2024-01-24 13:48:56,213] [INFO] Task started: HMMsearch
[2024-01-24 13:48:56,214] [INFO] Running command: hmmsearch --tblout GCF_000179595.2_ASM17959v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdd40743d-4280-4548-9dbb-cfc90e7193ca/dqc_reference/reference_markers.hmm GCF_000179595.2_ASM17959v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:48:56,543] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:48:56,545] [INFO] Found 6/6 markers.
[2024-01-24 13:48:56,594] [INFO] Query marker FASTA was written to GCF_000179595.2_ASM17959v2_genomic.fna/markers.fasta
[2024-01-24 13:48:56,594] [INFO] Task started: Blastn
[2024-01-24 13:48:56,594] [INFO] Running command: blastn -query GCF_000179595.2_ASM17959v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd40743d-4280-4548-9dbb-cfc90e7193ca/dqc_reference/reference_markers.fasta -out GCF_000179595.2_ASM17959v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:48:57,219] [INFO] Task succeeded: Blastn
[2024-01-24 13:48:57,224] [INFO] Selected 21 target genomes.
[2024-01-24 13:48:57,224] [INFO] Target genome list was writen to GCF_000179595.2_ASM17959v2_genomic.fna/target_genomes.txt
[2024-01-24 13:48:57,232] [INFO] Task started: fastANI
[2024-01-24 13:48:57,232] [INFO] Running command: fastANI --query /var/lib/cwl/stg44f86e0d-98b9-43b5-b47d-7c045d6075bb/GCF_000179595.2_ASM17959v2_genomic.fna.gz --refList GCF_000179595.2_ASM17959v2_genomic.fna/target_genomes.txt --output GCF_000179595.2_ASM17959v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:09,571] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:09,572] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdd40743d-4280-4548-9dbb-cfc90e7193ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:09,572] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdd40743d-4280-4548-9dbb-cfc90e7193ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:09,578] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:09,579] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:09,579] [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 cellulolyticus	strain=CD2	GCA_000179595.2	35830	35830	type	True	100.0	2047	2047	95	conclusive
Acetivibrio clariflavus	strain=DSM 19732	GCA_000237085.1	288965	288965	type	True	77.9814	399	2047	95	below_threshold
Acetivibrio straminisolvens	strain=JCM 21531	GCA_000521465.1	253314	253314	type	True	77.2647	134	2047	95	below_threshold
Acetivibrio thermocellus	strain=ATCC 27405	GCA_000015865.1	1515	1515	type	True	77.1537	87	2047	95	below_threshold
Acetivibrio mesophilus	strain=N2K1	GCA_004102745.1	2487273	2487273	type	True	77.1366	145	2047	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:09,580] [INFO] DFAST Taxonomy check result was written to GCF_000179595.2_ASM17959v2_genomic.fna/tc_result.tsv
[2024-01-24 13:49:09,581] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:09,581] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:09,582] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdd40743d-4280-4548-9dbb-cfc90e7193ca/dqc_reference/checkm_data
[2024-01-24 13:49:09,584] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:09,649] [INFO] Task started: CheckM
[2024-01-24 13:49:09,650] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000179595.2_ASM17959v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000179595.2_ASM17959v2_genomic.fna/checkm_input GCF_000179595.2_ASM17959v2_genomic.fna/checkm_result
[2024-01-24 13:49:50,724] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:50,725] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:50,747] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:50,748] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:50,748] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000179595.2_ASM17959v2_genomic.fna/markers.fasta)
[2024-01-24 13:49:50,749] [INFO] Task started: Blastn
[2024-01-24 13:49:50,749] [INFO] Running command: blastn -query GCF_000179595.2_ASM17959v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd40743d-4280-4548-9dbb-cfc90e7193ca/dqc_reference/reference_markers_gtdb.fasta -out GCF_000179595.2_ASM17959v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:51,768] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:51,772] [INFO] Selected 23 target genomes.
[2024-01-24 13:49:51,772] [INFO] Target genome list was writen to GCF_000179595.2_ASM17959v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:51,796] [INFO] Task started: fastANI
[2024-01-24 13:49:51,796] [INFO] Running command: fastANI --query /var/lib/cwl/stg44f86e0d-98b9-43b5-b47d-7c045d6075bb/GCF_000179595.2_ASM17959v2_genomic.fna.gz --refList GCF_000179595.2_ASM17959v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000179595.2_ASM17959v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:06,957] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:06,965] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:06,965] [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_000179595.2	s__Acetivibrio cellulolyticus	100.0	2047	2047	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__Acetivibrionaceae;g__Acetivibrio	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_012519925.1	s__Acetivibrio sp012519925	79.2404	472	2047	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__Acetivibrionaceae;g__Acetivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000237085.1	s__Acetivibrio clariflavus	77.9427	402	2047	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__Acetivibrionaceae;g__Acetivibrio	95.0	98.23	96.28	0.88	0.88	4	-
GCA_000521465.1	s__Hungateiclostridium straminisolvens	77.2542	136	2047	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_000015865.1	s__Hungateiclostridium thermocellum	77.1494	87	2047	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__Acetivibrionaceae;g__Hungateiclostridium	95.0	99.61	99.46	0.95	0.92	14	-
GCF_004102745.1	s__Hungateiclostridium mesophilum	77.1379	145	2047	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__Acetivibrionaceae;g__Hungateiclostridium	95.0	99.61	99.52	0.93	0.90	4	-
GCA_001512505.1	s__Hungateiclostridium sp001512505	76.6852	101	2047	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__Acetivibrionaceae;g__Hungateiclostridium	95.0	99.73	99.73	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:06,967] [INFO] GTDB search result was written to GCF_000179595.2_ASM17959v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:06,968] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:06,971] [INFO] DFAST_QC result json was written to GCF_000179595.2_ASM17959v2_genomic.fna/dqc_result.json
[2024-01-24 13:50:06,971] [INFO] DFAST_QC completed!
[2024-01-24 13:50:06,971] [INFO] Total running time: 0h1m24s