[2024-01-24 13:32:18,038] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:18,041] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:18,041] [INFO] DQC Reference Directory: /var/lib/cwl/stg6b0886e7-6fe3-44c5-8bad-f490bad3b03a/dqc_reference
[2024-01-24 13:32:19,450] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:19,451] [INFO] Task started: Prodigal
[2024-01-24 13:32:19,451] [INFO] Running command: gunzip -c /var/lib/cwl/stgb48b397c-09b6-4c76-be0f-54a0a31bd559/GCF_009707925.1_ASM970792v1_genomic.fna.gz | prodigal -d GCF_009707925.1_ASM970792v1_genomic.fna/cds.fna -a GCF_009707925.1_ASM970792v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:28,340] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:28,340] [INFO] Task started: HMMsearch
[2024-01-24 13:32:28,340] [INFO] Running command: hmmsearch --tblout GCF_009707925.1_ASM970792v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6b0886e7-6fe3-44c5-8bad-f490bad3b03a/dqc_reference/reference_markers.hmm GCF_009707925.1_ASM970792v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:28,608] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:28,610] [INFO] Found 6/6 markers.
[2024-01-24 13:32:28,646] [INFO] Query marker FASTA was written to GCF_009707925.1_ASM970792v1_genomic.fna/markers.fasta
[2024-01-24 13:32:28,647] [INFO] Task started: Blastn
[2024-01-24 13:32:28,647] [INFO] Running command: blastn -query GCF_009707925.1_ASM970792v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b0886e7-6fe3-44c5-8bad-f490bad3b03a/dqc_reference/reference_markers.fasta -out GCF_009707925.1_ASM970792v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:29,294] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:29,298] [INFO] Selected 13 target genomes.
[2024-01-24 13:32:29,299] [INFO] Target genome list was writen to GCF_009707925.1_ASM970792v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:29,307] [INFO] Task started: fastANI
[2024-01-24 13:32:29,308] [INFO] Running command: fastANI --query /var/lib/cwl/stgb48b397c-09b6-4c76-be0f-54a0a31bd559/GCF_009707925.1_ASM970792v1_genomic.fna.gz --refList GCF_009707925.1_ASM970792v1_genomic.fna/target_genomes.txt --output GCF_009707925.1_ASM970792v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:39,243] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:39,243] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6b0886e7-6fe3-44c5-8bad-f490bad3b03a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:39,244] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6b0886e7-6fe3-44c5-8bad-f490bad3b03a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:39,256] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:39,257] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:39,257] [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
Blautia luti	strain=DSM 14534	GCA_009707925.1	89014	89014	suspected-type	True	100.0	1211	1214	95	conclusive
Blautia wexlerae	strain=DSM 19850	GCA_025148125.1	418240	418240	suspected-type	True	86.6413	741	1214	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_000484655.1	418240	418240	suspected-type	True	86.5026	703	1214	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_000153905.1	40520	40520	type	True	82.8292	398	1214	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	82.7242	394	1214	95	below_threshold
Blautia massiliensis	strain=GD9	GCA_001487165.1	1737424	1737424	type	True	82.6204	454	1214	95	below_threshold
Blautia intestinalis	strain=27-44	GCA_014297355.1	2763028	2763028	type	True	81.611	382	1214	95	below_threshold
Jingyaoa shaoxingensis	strain=NSJ-46	GCA_014385005.1	2763671	2763671	type	True	81.3116	188	1214	95	below_threshold
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	79.3167	293	1214	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	79.1609	108	1214	95	below_threshold
Blautia marasmi	strain=Marseille-P2377	GCA_900258535.1	1917868	1917868	suspected-type	True	78.4533	115	1214	95	below_threshold
Diplocloster modestus	strain=ASD4241	GCA_019042245.1	2850322	2850322	type	True	77.0364	53	1214	95	below_threshold
Lactonifactor longoviformis	strain=DSM 17459	GCA_002915525.1	341220	341220	suspected-type	True	76.8575	70	1214	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:39,264] [INFO] DFAST Taxonomy check result was written to GCF_009707925.1_ASM970792v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:39,264] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:39,264] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:39,265] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6b0886e7-6fe3-44c5-8bad-f490bad3b03a/dqc_reference/checkm_data
[2024-01-24 13:32:39,266] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:39,308] [INFO] Task started: CheckM
[2024-01-24 13:32:39,308] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009707925.1_ASM970792v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009707925.1_ASM970792v1_genomic.fna/checkm_input GCF_009707925.1_ASM970792v1_genomic.fna/checkm_result
[2024-01-24 13:33:13,529] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:13,530] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:13,548] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:13,549] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:13,550] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009707925.1_ASM970792v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:13,550] [INFO] Task started: Blastn
[2024-01-24 13:33:13,550] [INFO] Running command: blastn -query GCF_009707925.1_ASM970792v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b0886e7-6fe3-44c5-8bad-f490bad3b03a/dqc_reference/reference_markers_gtdb.fasta -out GCF_009707925.1_ASM970792v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:14,795] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:14,799] [INFO] Selected 7 target genomes.
[2024-01-24 13:33:14,799] [INFO] Target genome list was writen to GCF_009707925.1_ASM970792v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:14,805] [INFO] Task started: fastANI
[2024-01-24 13:33:14,806] [INFO] Running command: fastANI --query /var/lib/cwl/stgb48b397c-09b6-4c76-be0f-54a0a31bd559/GCF_009707925.1_ASM970792v1_genomic.fna.gz --refList GCF_009707925.1_ASM970792v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009707925.1_ASM970792v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:21,444] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:21,451] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:21,451] [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_009707925.1	s__Blautia_A luti	100.0	1211	1214	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.33	97.04	0.87	0.84	5	conclusive
GCF_003477525.1	s__Blautia_A sp003477525	87.1252	784	1214	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	99.30	98.60	0.90	0.81	3	-
GCF_018919065.1	s__Blautia_A sp018919065	86.7956	642	1214	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013300825.1	s__Blautia_A wexlerae_B	86.6259	722	1214	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.68	98.07	0.89	0.86	5	-
GCF_000484655.1	s__Blautia_A wexlerae	86.4944	704	1214	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	97.38	96.15	0.76	0.65	140	-
GCF_003471165.1	s__Blautia_A sp003471165	86.107	750	1214	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.40	97.74	0.83	0.79	20	-
GCA_905209435.1	s__Blautia_A sp905209435	84.5451	571	1214	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:21,453] [INFO] GTDB search result was written to GCF_009707925.1_ASM970792v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:21,453] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:21,456] [INFO] DFAST_QC result json was written to GCF_009707925.1_ASM970792v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:21,457] [INFO] DFAST_QC completed!
[2024-01-24 13:33:21,457] [INFO] Total running time: 0h1m3s