[2024-01-24 10:47:09,476] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:09,478] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:09,479] [INFO] DQC Reference Directory: /var/lib/cwl/stg71974289-eecf-4942-a069-88c66561fc51/dqc_reference
[2024-01-24 10:47:11,835] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:11,913] [INFO] Task started: Prodigal
[2024-01-24 10:47:11,913] [INFO] Running command: gunzip -c /var/lib/cwl/stg3e791989-5e93-40bc-b653-c466d0771e0c/GCF_003208175.1_ASM320817v1_genomic.fna.gz | prodigal -d GCF_003208175.1_ASM320817v1_genomic.fna/cds.fna -a GCF_003208175.1_ASM320817v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:21,474] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:21,475] [INFO] Task started: HMMsearch
[2024-01-24 10:47:21,475] [INFO] Running command: hmmsearch --tblout GCF_003208175.1_ASM320817v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg71974289-eecf-4942-a069-88c66561fc51/dqc_reference/reference_markers.hmm GCF_003208175.1_ASM320817v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:21,757] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:21,758] [INFO] Found 6/6 markers.
[2024-01-24 10:47:21,798] [INFO] Query marker FASTA was written to GCF_003208175.1_ASM320817v1_genomic.fna/markers.fasta
[2024-01-24 10:47:21,798] [INFO] Task started: Blastn
[2024-01-24 10:47:21,798] [INFO] Running command: blastn -query GCF_003208175.1_ASM320817v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg71974289-eecf-4942-a069-88c66561fc51/dqc_reference/reference_markers.fasta -out GCF_003208175.1_ASM320817v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:22,488] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:22,493] [INFO] Selected 17 target genomes.
[2024-01-24 10:47:22,493] [INFO] Target genome list was writen to GCF_003208175.1_ASM320817v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:23,014] [INFO] Task started: fastANI
[2024-01-24 10:47:23,014] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e791989-5e93-40bc-b653-c466d0771e0c/GCF_003208175.1_ASM320817v1_genomic.fna.gz --refList GCF_003208175.1_ASM320817v1_genomic.fna/target_genomes.txt --output GCF_003208175.1_ASM320817v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:34,901] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:34,901] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg71974289-eecf-4942-a069-88c66561fc51/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:34,902] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg71974289-eecf-4942-a069-88c66561fc51/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:34,915] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:47:34,915] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:34,915] [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
Ruminiclostridium sufflavum	strain=DSM 19573	GCA_003208175.1	396504	396504	type	True	100.0	1431	1433	95	conclusive
Ruminiclostridium herbifermentans	strain=MA18	GCA_005473905.2	2488810	2488810	type	True	79.1316	546	1433	95	below_threshold
Ruminiclostridium papyrosolvens	strain=DSM 2782	GCA_000175795.2	29362	29362	type	True	77.5203	192	1433	95	below_threshold
Ruminiclostridium josui	strain=JCM 17888	GCA_000526495.1	1499	1499	type	True	77.4889	188	1433	95	below_threshold
Ruminiclostridium cellulolyticum	strain=H10; ATCC 35319	GCA_000022065.1	1521	1521	type	True	77.2656	191	1433	95	below_threshold
Ruminiclostridium cellobioparum	strain=ATCC 15832	GCA_000621505.1	29355	29355	type	True	77.265	196	1433	95	below_threshold
Ruminiclostridium hungatei	strain=DSM 14427	GCA_002051585.1	48256	48256	type	True	77.2558	199	1433	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:34,917] [INFO] DFAST Taxonomy check result was written to GCF_003208175.1_ASM320817v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:34,918] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:34,918] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:34,918] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg71974289-eecf-4942-a069-88c66561fc51/dqc_reference/checkm_data
[2024-01-24 10:47:34,919] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:34,967] [INFO] Task started: CheckM
[2024-01-24 10:47:34,967] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003208175.1_ASM320817v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003208175.1_ASM320817v1_genomic.fna/checkm_input GCF_003208175.1_ASM320817v1_genomic.fna/checkm_result
[2024-01-24 10:48:09,513] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:09,514] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:09,532] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:09,533] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:09,533] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003208175.1_ASM320817v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:09,533] [INFO] Task started: Blastn
[2024-01-24 10:48:09,534] [INFO] Running command: blastn -query GCF_003208175.1_ASM320817v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg71974289-eecf-4942-a069-88c66561fc51/dqc_reference/reference_markers_gtdb.fasta -out GCF_003208175.1_ASM320817v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:10,613] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:10,619] [INFO] Selected 21 target genomes.
[2024-01-24 10:48:10,619] [INFO] Target genome list was writen to GCF_003208175.1_ASM320817v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:10,944] [INFO] Task started: fastANI
[2024-01-24 10:48:10,944] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e791989-5e93-40bc-b653-c466d0771e0c/GCF_003208175.1_ASM320817v1_genomic.fna.gz --refList GCF_003208175.1_ASM320817v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003208175.1_ASM320817v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:22,719] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:22,726] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:22,727] [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_003208175.1	s__Ruminiclostridium sufflavum	100.0	1431	1433	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__DSM-27016;g__Ruminiclostridium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_005473905.2	s__Ruminiclostridium herbifermentans	79.1455	546	1433	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__DSM-27016;g__Ruminiclostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000244875.1	s__Ruminiclostridium sp000244875	77.6049	181	1433	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__DSM-27016;g__Ruminiclostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000175795.2	s__Ruminiclostridium papyrosolvens	77.517	193	1433	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__DSM-27016;g__Ruminiclostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000526495.1	s__Ruminiclostridium josui	77.4887	188	1433	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__DSM-27016;g__Ruminiclostridium	95.0	99.95	99.95	1.00	1.00	2	-
GCF_002051585.1	s__Ruminiclostridium hungatei	77.282	197	1433	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__DSM-27016;g__Ruminiclostridium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:22,729] [INFO] GTDB search result was written to GCF_003208175.1_ASM320817v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:22,730] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:22,732] [INFO] DFAST_QC result json was written to GCF_003208175.1_ASM320817v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:22,733] [INFO] DFAST_QC completed!
[2024-01-24 10:48:22,733] [INFO] Total running time: 0h1m13s