[2024-01-24 13:27:58,784] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:58,786] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:58,787] [INFO] DQC Reference Directory: /var/lib/cwl/stge397ad66-aba7-4d94-92b5-232f496ba398/dqc_reference
[2024-01-24 13:28:00,004] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:00,005] [INFO] Task started: Prodigal
[2024-01-24 13:28:00,005] [INFO] Running command: gunzip -c /var/lib/cwl/stg8cb0db04-92f7-46a6-b504-070ab12fb7c6/GCF_000621285.1_ASM62128v1_genomic.fna.gz | prodigal -d GCF_000621285.1_ASM62128v1_genomic.fna/cds.fna -a GCF_000621285.1_ASM62128v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:09,517] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:09,517] [INFO] Task started: HMMsearch
[2024-01-24 13:28:09,517] [INFO] Running command: hmmsearch --tblout GCF_000621285.1_ASM62128v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge397ad66-aba7-4d94-92b5-232f496ba398/dqc_reference/reference_markers.hmm GCF_000621285.1_ASM62128v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:09,813] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:09,815] [INFO] Found 6/6 markers.
[2024-01-24 13:28:09,853] [INFO] Query marker FASTA was written to GCF_000621285.1_ASM62128v1_genomic.fna/markers.fasta
[2024-01-24 13:28:09,853] [INFO] Task started: Blastn
[2024-01-24 13:28:09,853] [INFO] Running command: blastn -query GCF_000621285.1_ASM62128v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge397ad66-aba7-4d94-92b5-232f496ba398/dqc_reference/reference_markers.fasta -out GCF_000621285.1_ASM62128v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:10,439] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:10,442] [INFO] Selected 12 target genomes.
[2024-01-24 13:28:10,443] [INFO] Target genome list was writen to GCF_000621285.1_ASM62128v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:10,455] [INFO] Task started: fastANI
[2024-01-24 13:28:10,455] [INFO] Running command: fastANI --query /var/lib/cwl/stg8cb0db04-92f7-46a6-b504-070ab12fb7c6/GCF_000621285.1_ASM62128v1_genomic.fna.gz --refList GCF_000621285.1_ASM62128v1_genomic.fna/target_genomes.txt --output GCF_000621285.1_ASM62128v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:18,900] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:18,900] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge397ad66-aba7-4d94-92b5-232f496ba398/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:18,900] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge397ad66-aba7-4d94-92b5-232f496ba398/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:18,907] [INFO] Found 4 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:28:18,907] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:18,907] [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
Ruminococcus albus	strain=DSM 20455	GCA_000621285.1	1264	1264	suspected-type	True	100.0	1379	1383	95	conclusive
Ruminococcus albus	strain=7	GCA_000179635.2	1264	1264	suspected-type	True	99.9608	1368	1383	95	conclusive
Ruminococcus bicirculans	strain=80/3	GCA_000723465.1	1160721	1160721	type	True	77.6063	137	1383	95	below_threshold
Ruminococcus flavefaciens	strain=ATCC 19208	GCA_000518765.1	1265	1265	suspected-type	True	77.015	108	1383	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:18,908] [INFO] DFAST Taxonomy check result was written to GCF_000621285.1_ASM62128v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:18,909] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:18,909] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:18,909] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge397ad66-aba7-4d94-92b5-232f496ba398/dqc_reference/checkm_data
[2024-01-24 13:28:18,911] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:18,953] [INFO] Task started: CheckM
[2024-01-24 13:28:18,953] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000621285.1_ASM62128v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000621285.1_ASM62128v1_genomic.fna/checkm_input GCF_000621285.1_ASM62128v1_genomic.fna/checkm_result
[2024-01-24 13:28:53,788] [INFO] Task succeeded: CheckM
[2024-01-24 13:28:53,790] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:28:53,810] [INFO] ===== Completeness check finished =====
[2024-01-24 13:28:53,810] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:28:53,811] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000621285.1_ASM62128v1_genomic.fna/markers.fasta)
[2024-01-24 13:28:53,811] [INFO] Task started: Blastn
[2024-01-24 13:28:53,811] [INFO] Running command: blastn -query GCF_000621285.1_ASM62128v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge397ad66-aba7-4d94-92b5-232f496ba398/dqc_reference/reference_markers_gtdb.fasta -out GCF_000621285.1_ASM62128v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:54,683] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:54,687] [INFO] Selected 10 target genomes.
[2024-01-24 13:28:54,687] [INFO] Target genome list was writen to GCF_000621285.1_ASM62128v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:28:54,715] [INFO] Task started: fastANI
[2024-01-24 13:28:54,716] [INFO] Running command: fastANI --query /var/lib/cwl/stg8cb0db04-92f7-46a6-b504-070ab12fb7c6/GCF_000621285.1_ASM62128v1_genomic.fna.gz --refList GCF_000621285.1_ASM62128v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000621285.1_ASM62128v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:03,238] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:03,246] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:03,247] [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_000179635.2	s__Ruminococcus_D albus	99.9608	1368	1383	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	98.29	97.69	0.91	0.87	8	conclusive
GCF_000526775.1	s__Ruminococcus_D albus_A	87.5595	877	1383	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	97.64	97.22	0.89	0.80	5	-
GCF_900112155.1	s__Ruminococcus_D albus_D	84.4002	824	1383	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109655.1	s__Ruminococcus_D albus_B	84.0524	758	1383	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	96.54	96.54	0.90	0.90	2	-
GCA_017464355.1	s__Ruminococcus_D sp017464355	80.4233	467	1383	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902788785.1	s__Ruminococcus_D sp902788785	79.9537	357	1383	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	98.09	97.87	0.85	0.73	4	-
GCA_902786965.1	s__Ruminococcus_D sp902786965	77.2821	138	1383	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	97.48	97.28	0.83	0.79	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:03,249] [INFO] GTDB search result was written to GCF_000621285.1_ASM62128v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:03,249] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:03,252] [INFO] DFAST_QC result json was written to GCF_000621285.1_ASM62128v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:03,252] [INFO] DFAST_QC completed!
[2024-01-24 13:29:03,252] [INFO] Total running time: 0h1m4s