[2024-01-24 11:26:20,813] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:20,816] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:20,816] [INFO] DQC Reference Directory: /var/lib/cwl/stg31bc1928-de4e-4a9a-b07c-114c07a7460d/dqc_reference
[2024-01-24 11:26:22,038] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:22,039] [INFO] Task started: Prodigal
[2024-01-24 11:26:22,039] [INFO] Running command: gunzip -c /var/lib/cwl/stgba0416bb-e2be-464c-b168-b1b5fd1392dd/GCF_021044755.1_ASM2104475v1_genomic.fna.gz | prodigal -d GCF_021044755.1_ASM2104475v1_genomic.fna/cds.fna -a GCF_021044755.1_ASM2104475v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:29,932] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:29,933] [INFO] Task started: HMMsearch
[2024-01-24 11:26:29,933] [INFO] Running command: hmmsearch --tblout GCF_021044755.1_ASM2104475v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg31bc1928-de4e-4a9a-b07c-114c07a7460d/dqc_reference/reference_markers.hmm GCF_021044755.1_ASM2104475v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:30,249] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:30,251] [INFO] Found 6/6 markers.
[2024-01-24 11:26:30,299] [INFO] Query marker FASTA was written to GCF_021044755.1_ASM2104475v1_genomic.fna/markers.fasta
[2024-01-24 11:26:30,300] [INFO] Task started: Blastn
[2024-01-24 11:26:30,300] [INFO] Running command: blastn -query GCF_021044755.1_ASM2104475v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg31bc1928-de4e-4a9a-b07c-114c07a7460d/dqc_reference/reference_markers.fasta -out GCF_021044755.1_ASM2104475v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:30,896] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:30,899] [INFO] Selected 22 target genomes.
[2024-01-24 11:26:30,899] [INFO] Target genome list was writen to GCF_021044755.1_ASM2104475v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:30,913] [INFO] Task started: fastANI
[2024-01-24 11:26:30,913] [INFO] Running command: fastANI --query /var/lib/cwl/stgba0416bb-e2be-464c-b168-b1b5fd1392dd/GCF_021044755.1_ASM2104475v1_genomic.fna.gz --refList GCF_021044755.1_ASM2104475v1_genomic.fna/target_genomes.txt --output GCF_021044755.1_ASM2104475v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:44,439] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:44,439] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg31bc1928-de4e-4a9a-b07c-114c07a7460d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:44,440] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg31bc1928-de4e-4a9a-b07c-114c07a7460d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:44,451] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:26:44,452] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:26:44,452] [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
Qiania dongpingensis	strain=NSJ-38	GCA_014337195.1	2763669	2763669	type	True	90.9886	840	1009	95	below_threshold
Eisenbergiella massiliensis	strain=AT11	GCA_900243045.1	1720294	1720294	type	True	77.4645	53	1009	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_025149285.1	154046	154046	suspected-type	True	77.3833	54	1009	95	below_threshold
Enterocloster clostridioformis	strain=NCTC11224	GCA_900447015.1	1531	1531	suspected-type	True	76.6799	59	1009	95	below_threshold
Enterocloster clostridioformis	strain=FDAARGOS_1529	GCA_020297485.1	1531	1531	suspected-type	True	76.6452	60	1009	95	below_threshold
Eisenbergiella tayi	strain=DSM 26961	GCA_001881565.1	1432052	1432052	type	True	76.6079	60	1009	95	below_threshold
Cuneatibacter caecimuris	strain=DSM 29486	GCA_004216775.1	1796618	1796618	type	True	76.5826	54	1009	95	below_threshold
Enterocloster clostridioformis	strain=ATCC 25537	GCA_900113155.1	1531	1531	type	True	76.4487	61	1009	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:44,453] [INFO] DFAST Taxonomy check result was written to GCF_021044755.1_ASM2104475v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:44,454] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:44,454] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:44,454] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg31bc1928-de4e-4a9a-b07c-114c07a7460d/dqc_reference/checkm_data
[2024-01-24 11:26:44,455] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:44,489] [INFO] Task started: CheckM
[2024-01-24 11:26:44,490] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021044755.1_ASM2104475v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021044755.1_ASM2104475v1_genomic.fna/checkm_input GCF_021044755.1_ASM2104475v1_genomic.fna/checkm_result
[2024-01-24 11:27:13,683] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:13,685] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:13,705] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:13,706] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:13,706] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021044755.1_ASM2104475v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:13,707] [INFO] Task started: Blastn
[2024-01-24 11:27:13,707] [INFO] Running command: blastn -query GCF_021044755.1_ASM2104475v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg31bc1928-de4e-4a9a-b07c-114c07a7460d/dqc_reference/reference_markers_gtdb.fasta -out GCF_021044755.1_ASM2104475v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:14,625] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:14,630] [INFO] Selected 15 target genomes.
[2024-01-24 11:27:14,631] [INFO] Target genome list was writen to GCF_021044755.1_ASM2104475v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:14,647] [INFO] Task started: fastANI
[2024-01-24 11:27:14,648] [INFO] Running command: fastANI --query /var/lib/cwl/stgba0416bb-e2be-464c-b168-b1b5fd1392dd/GCF_021044755.1_ASM2104475v1_genomic.fna.gz --refList GCF_021044755.1_ASM2104475v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021044755.1_ASM2104475v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:23,137] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:23,157] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:27:23,157] [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_902363445.1	s__Paralachnospira sp902363445	92.0372	833	1009	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Paralachnospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014337195.1	s__Paralachnospira sp014337195	91.0055	839	1009	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Paralachnospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005845265.1	s__Hungatella sp005845265	78.318	50	1009	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Hungatella	95.0	98.89	98.68	0.87	0.80	12	-
GCF_904379015.1	s__Paralachnospira caecorum	78.2442	251	1009	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Paralachnospira	95.0	99.98	99.98	0.92	0.92	2	-
GCA_910588815.1	s__Paralachnospira sp910588815	77.4808	177	1009	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Paralachnospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904420245.1	s__Paralachnospira avium	77.3083	207	1009	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Paralachnospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587905.1	s__Paralachnospira sp910587905	77.1958	156	1009	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Paralachnospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216775.1	s__Cuneatibacter caecimuris	76.5826	54	1009	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Cuneatibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019119595.1	s__Eisenbergiella merdavium	76.1441	52	1009	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eisenbergiella	95.0	98.10	98.10	0.87	0.87	2	-
GCA_014385265.1	s__Copromonas sp000435795	75.9827	55	1009	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Copromonas	95.0	98.24	96.73	0.89	0.84	6	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:23,159] [INFO] GTDB search result was written to GCF_021044755.1_ASM2104475v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:23,160] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:23,163] [INFO] DFAST_QC result json was written to GCF_021044755.1_ASM2104475v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:23,164] [INFO] DFAST_QC completed!
[2024-01-24 11:27:23,164] [INFO] Total running time: 0h1m2s