[2024-01-25 20:17:35,469] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:17:35,472] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:17:35,472] [INFO] DQC Reference Directory: /var/lib/cwl/stge1e4679f-9bf5-4399-ae2b-9531b5cf8efa/dqc_reference
[2024-01-25 20:17:36,595] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:17:36,596] [INFO] Task started: Prodigal
[2024-01-25 20:17:36,596] [INFO] Running command: gunzip -c /var/lib/cwl/stg90100464-e232-42f9-a329-660e4ccc7b4f/GCF_002735925.1_ASM273592v1_genomic.fna.gz | prodigal -d GCF_002735925.1_ASM273592v1_genomic.fna/cds.fna -a GCF_002735925.1_ASM273592v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:17:42,386] [INFO] Task succeeded: Prodigal
[2024-01-25 20:17:42,387] [INFO] Task started: HMMsearch
[2024-01-25 20:17:42,387] [INFO] Running command: hmmsearch --tblout GCF_002735925.1_ASM273592v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge1e4679f-9bf5-4399-ae2b-9531b5cf8efa/dqc_reference/reference_markers.hmm GCF_002735925.1_ASM273592v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:17:42,608] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:17:42,610] [INFO] Found 6/6 markers.
[2024-01-25 20:17:42,639] [INFO] Query marker FASTA was written to GCF_002735925.1_ASM273592v1_genomic.fna/markers.fasta
[2024-01-25 20:17:42,639] [INFO] Task started: Blastn
[2024-01-25 20:17:42,640] [INFO] Running command: blastn -query GCF_002735925.1_ASM273592v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge1e4679f-9bf5-4399-ae2b-9531b5cf8efa/dqc_reference/reference_markers.fasta -out GCF_002735925.1_ASM273592v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:17:43,214] [INFO] Task succeeded: Blastn
[2024-01-25 20:17:43,216] [INFO] Selected 28 target genomes.
[2024-01-25 20:17:43,217] [INFO] Target genome list was writen to GCF_002735925.1_ASM273592v1_genomic.fna/target_genomes.txt
[2024-01-25 20:17:43,233] [INFO] Task started: fastANI
[2024-01-25 20:17:43,233] [INFO] Running command: fastANI --query /var/lib/cwl/stg90100464-e232-42f9-a329-660e4ccc7b4f/GCF_002735925.1_ASM273592v1_genomic.fna.gz --refList GCF_002735925.1_ASM273592v1_genomic.fna/target_genomes.txt --output GCF_002735925.1_ASM273592v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:17:58,515] [INFO] Task succeeded: fastANI
[2024-01-25 20:17:58,515] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge1e4679f-9bf5-4399-ae2b-9531b5cf8efa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:17:58,516] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge1e4679f-9bf5-4399-ae2b-9531b5cf8efa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:17:58,521] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:17:58,521] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:17:58,521] [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
Cellulosilyticum lentocellum	strain=DSM 5427	GCA_000178835.2	29360	29360	type	True	78.994	258	1218	95	below_threshold
Cellulosilyticum ruminicola	strain=JCM 14822	GCA_001311925.1	425254	425254	type	True	77.7692	196	1218	95	below_threshold
Defluviitalea phaphyphila	strain=Alg1	GCA_001466305.1	1473580	1473580	type	True	76.2794	51	1218	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:17:58,523] [INFO] DFAST Taxonomy check result was written to GCF_002735925.1_ASM273592v1_genomic.fna/tc_result.tsv
[2024-01-25 20:17:58,524] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:17:58,524] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:17:58,524] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge1e4679f-9bf5-4399-ae2b-9531b5cf8efa/dqc_reference/checkm_data
[2024-01-25 20:17:58,525] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:17:58,564] [INFO] Task started: CheckM
[2024-01-25 20:17:58,565] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002735925.1_ASM273592v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002735925.1_ASM273592v1_genomic.fna/checkm_input GCF_002735925.1_ASM273592v1_genomic.fna/checkm_result
[2024-01-25 20:18:21,231] [INFO] Task succeeded: CheckM
[2024-01-25 20:18:21,233] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:18:21,265] [INFO] ===== Completeness check finished =====
[2024-01-25 20:18:21,265] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:18:21,266] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002735925.1_ASM273592v1_genomic.fna/markers.fasta)
[2024-01-25 20:18:21,267] [INFO] Task started: Blastn
[2024-01-25 20:18:21,267] [INFO] Running command: blastn -query GCF_002735925.1_ASM273592v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge1e4679f-9bf5-4399-ae2b-9531b5cf8efa/dqc_reference/reference_markers_gtdb.fasta -out GCF_002735925.1_ASM273592v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:18:22,258] [INFO] Task succeeded: Blastn
[2024-01-25 20:18:22,261] [INFO] Selected 23 target genomes.
[2024-01-25 20:18:22,261] [INFO] Target genome list was writen to GCF_002735925.1_ASM273592v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:18:22,289] [INFO] Task started: fastANI
[2024-01-25 20:18:22,290] [INFO] Running command: fastANI --query /var/lib/cwl/stg90100464-e232-42f9-a329-660e4ccc7b4f/GCF_002735925.1_ASM273592v1_genomic.fna.gz --refList GCF_002735925.1_ASM273592v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002735925.1_ASM273592v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:18:35,731] [INFO] Task succeeded: fastANI
[2024-01-25 20:18:35,740] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:18:35,740] [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_002735925.1	s__Cellulosilyticum sp002735925	100.0	1214	1218	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Cellulosilyticaceae;g__Cellulosilyticum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000178835.2	s__Cellulosilyticum lentocellum	79.0501	259	1218	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Cellulosilyticaceae;g__Cellulosilyticum	95.0	97.43	97.43	0.84	0.84	2	-
GCA_014384995.1	s__Niameybacter stercoravium	77.8517	143	1218	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Cellulosilyticaceae;g__Niameybacter	95.0	97.76	95.05	0.90	0.86	8	-
GCA_015058045.1	s__Cellulosilyticum sp015058045	77.8126	181	1218	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Cellulosilyticaceae;g__Cellulosilyticum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900095725.1	s__FMMP01 sp900095725	77.8064	187	1218	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Cellulosilyticaceae;g__FMMP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018883705.1	s__Cellulosilyticum pullistercoris	77.7888	160	1218	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Cellulosilyticaceae;g__Cellulosilyticum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001311925.1	s__Cellulosilyticum ruminicola	77.7885	194	1218	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Cellulosilyticaceae;g__Cellulosilyticum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017941635.1	s__Cellulosilyticum sp017941635	77.6031	175	1218	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Cellulosilyticaceae;g__Cellulosilyticum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900551325.1	s__Niameybacter sp900551325	77.4411	151	1218	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Cellulosilyticaceae;g__Niameybacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001282685.1	s__Niameybacter massiliensis	77.4254	167	1218	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Cellulosilyticaceae;g__Niameybacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900556665.1	s__Cellulosilyticum sp900556665	77.2684	104	1218	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Cellulosilyticaceae;g__Cellulosilyticum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017421915.1	s__Cellulosilyticum sp017421915	77.0363	136	1218	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Cellulosilyticaceae;g__Cellulosilyticum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001466305.1	s__Defluviitalea phaphyphila	76.2922	52	1218	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Defluviitaleaceae;g__Defluviitalea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:18:35,742] [INFO] GTDB search result was written to GCF_002735925.1_ASM273592v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:18:35,742] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:18:35,746] [INFO] DFAST_QC result json was written to GCF_002735925.1_ASM273592v1_genomic.fna/dqc_result.json
[2024-01-25 20:18:35,747] [INFO] DFAST_QC completed!
[2024-01-25 20:18:35,747] [INFO] Total running time: 0h1m0s