[2024-01-24 13:33:41,059] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:33:41,061] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:33:41,061] [INFO] DQC Reference Directory: /var/lib/cwl/stg23eb9383-00c9-4cc1-b0bb-186cd9a4061a/dqc_reference
[2024-01-24 13:33:42,305] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:33:42,306] [INFO] Task started: Prodigal
[2024-01-24 13:33:42,306] [INFO] Running command: gunzip -c /var/lib/cwl/stg7296cf01-202e-48b7-9c36-4bf5715c5519/GCF_000621505.1_ASM62150v1_genomic.fna.gz | prodigal -d GCF_000621505.1_ASM62150v1_genomic.fna/cds.fna -a GCF_000621505.1_ASM62150v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:33:56,353] [INFO] Task succeeded: Prodigal
[2024-01-24 13:33:56,354] [INFO] Task started: HMMsearch
[2024-01-24 13:33:56,354] [INFO] Running command: hmmsearch --tblout GCF_000621505.1_ASM62150v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg23eb9383-00c9-4cc1-b0bb-186cd9a4061a/dqc_reference/reference_markers.hmm GCF_000621505.1_ASM62150v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:33:56,701] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:33:56,702] [INFO] Found 6/6 markers.
[2024-01-24 13:33:56,750] [INFO] Query marker FASTA was written to GCF_000621505.1_ASM62150v1_genomic.fna/markers.fasta
[2024-01-24 13:33:56,751] [INFO] Task started: Blastn
[2024-01-24 13:33:56,751] [INFO] Running command: blastn -query GCF_000621505.1_ASM62150v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg23eb9383-00c9-4cc1-b0bb-186cd9a4061a/dqc_reference/reference_markers.fasta -out GCF_000621505.1_ASM62150v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:57,372] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:57,376] [INFO] Selected 10 target genomes.
[2024-01-24 13:33:57,377] [INFO] Target genome list was writen to GCF_000621505.1_ASM62150v1_genomic.fna/target_genomes.txt
[2024-01-24 13:33:57,394] [INFO] Task started: fastANI
[2024-01-24 13:33:57,395] [INFO] Running command: fastANI --query /var/lib/cwl/stg7296cf01-202e-48b7-9c36-4bf5715c5519/GCF_000621505.1_ASM62150v1_genomic.fna.gz --refList GCF_000621505.1_ASM62150v1_genomic.fna/target_genomes.txt --output GCF_000621505.1_ASM62150v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:34:07,568] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:07,568] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg23eb9383-00c9-4cc1-b0bb-186cd9a4061a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:34:07,569] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg23eb9383-00c9-4cc1-b0bb-186cd9a4061a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:34:07,581] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:34:07,581] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:34:07,582] [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 cellobioparum	strain=ATCC 15832	GCA_000621505.1	29355	29355	type	True	100.0	1999	2004	95	conclusive
Ruminiclostridium cellobioparum subsp. termitidis	strain=CT1112	GCA_000350485.1	29371	29355	type	True	96.5939	1664	2004	95	conclusive
Ruminiclostridium hungatei	strain=DSM 14427	GCA_002051585.1	48256	48256	type	True	79.2936	591	2004	95	below_threshold
Ruminiclostridium papyrosolvens	strain=DSM 2782	GCA_000175795.2	29362	29362	type	True	78.092	231	2004	95	below_threshold
Ruminiclostridium cellulolyticum	strain=H10; ATCC 35319	GCA_000022065.1	1521	1521	type	True	77.9454	236	2004	95	below_threshold
Ruminiclostridium josui	strain=JCM 17888	GCA_000526495.1	1499	1499	type	True	77.7215	185	2004	95	below_threshold
Ruminiclostridium josui	strain=JCM 17888	GCA_001311015.1	1499	1499	type	True	77.6192	182	2004	95	below_threshold
Ruminiclostridium herbifermentans	strain=MA18	GCA_005473905.2	2488810	2488810	type	True	77.2746	156	2004	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:34:07,584] [INFO] DFAST Taxonomy check result was written to GCF_000621505.1_ASM62150v1_genomic.fna/tc_result.tsv
[2024-01-24 13:34:07,585] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:34:07,585] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:34:07,585] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg23eb9383-00c9-4cc1-b0bb-186cd9a4061a/dqc_reference/checkm_data
[2024-01-24 13:34:07,587] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:34:07,647] [INFO] Task started: CheckM
[2024-01-24 13:34:07,647] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000621505.1_ASM62150v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000621505.1_ASM62150v1_genomic.fna/checkm_input GCF_000621505.1_ASM62150v1_genomic.fna/checkm_result
[2024-01-24 13:34:52,841] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:52,843] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:52,871] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:52,872] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:52,872] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000621505.1_ASM62150v1_genomic.fna/markers.fasta)
[2024-01-24 13:34:52,872] [INFO] Task started: Blastn
[2024-01-24 13:34:52,873] [INFO] Running command: blastn -query GCF_000621505.1_ASM62150v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg23eb9383-00c9-4cc1-b0bb-186cd9a4061a/dqc_reference/reference_markers_gtdb.fasta -out GCF_000621505.1_ASM62150v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:53,849] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:53,853] [INFO] Selected 13 target genomes.
[2024-01-24 13:34:53,853] [INFO] Target genome list was writen to GCF_000621505.1_ASM62150v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:53,954] [INFO] Task started: fastANI
[2024-01-24 13:34:53,955] [INFO] Running command: fastANI --query /var/lib/cwl/stg7296cf01-202e-48b7-9c36-4bf5715c5519/GCF_000621505.1_ASM62150v1_genomic.fna.gz --refList GCF_000621505.1_ASM62150v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000621505.1_ASM62150v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:35:05,199] [INFO] Task succeeded: fastANI
[2024-01-24 13:35:05,213] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:35:05,213] [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_000621505.1	s__Ruminiclostridium cellobioparum	100.0	1998	2004	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__DSM-27016;g__Ruminiclostridium	96.6072	98.83	98.83	0.92	0.92	2	conclusive
GCF_000350485.1	s__Ruminiclostridium termitidis	96.5857	1665	2004	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Acetivibrionales;f__DSM-27016;g__Ruminiclostridium	96.6072	N/A	N/A	N/A	N/A	1	-
GCF_002051585.1	s__Ruminiclostridium hungatei	79.2935	591	2004	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	78.0999	229	2004	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_000022065.1	s__Ruminiclostridium cellulolyticum	77.9376	236	2004	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_000421965.1	s__Ruminiclostridium papyrosolvens_A	77.8251	213	2004	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	77.7215	185	2004	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_000244875.1	s__Ruminiclostridium sp000244875	77.697	244	2004	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_005473905.2	s__Ruminiclostridium herbifermentans	77.2579	155	2004	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 13:35:05,221] [INFO] GTDB search result was written to GCF_000621505.1_ASM62150v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:35:05,221] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:35:05,225] [INFO] DFAST_QC result json was written to GCF_000621505.1_ASM62150v1_genomic.fna/dqc_result.json
[2024-01-24 13:35:05,226] [INFO] DFAST_QC completed!
[2024-01-24 13:35:05,226] [INFO] Total running time: 0h1m24s