[2024-01-25 18:42:05,378] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:42:05,379] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:42:05,379] [INFO] DQC Reference Directory: /var/lib/cwl/stge99e7ab2-dbbf-405e-998a-cb4e25ff797d/dqc_reference
[2024-01-25 18:42:06,481] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:42:06,484] [INFO] Task started: Prodigal
[2024-01-25 18:42:06,484] [INFO] Running command: gunzip -c /var/lib/cwl/stg62e76f0a-683f-4ccb-b621-2ecd686e2eb2/GCF_000175795.2_ASM17579v2_genomic.fna.gz | prodigal -d GCF_000175795.2_ASM17579v2_genomic.fna/cds.fna -a GCF_000175795.2_ASM17579v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:42:15,354] [INFO] Task succeeded: Prodigal
[2024-01-25 18:42:15,354] [INFO] Task started: HMMsearch
[2024-01-25 18:42:15,355] [INFO] Running command: hmmsearch --tblout GCF_000175795.2_ASM17579v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge99e7ab2-dbbf-405e-998a-cb4e25ff797d/dqc_reference/reference_markers.hmm GCF_000175795.2_ASM17579v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:42:15,620] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:42:15,621] [INFO] Found 6/6 markers.
[2024-01-25 18:42:15,660] [INFO] Query marker FASTA was written to GCF_000175795.2_ASM17579v2_genomic.fna/markers.fasta
[2024-01-25 18:42:15,660] [INFO] Task started: Blastn
[2024-01-25 18:42:15,660] [INFO] Running command: blastn -query GCF_000175795.2_ASM17579v2_genomic.fna/markers.fasta -db /var/lib/cwl/stge99e7ab2-dbbf-405e-998a-cb4e25ff797d/dqc_reference/reference_markers.fasta -out GCF_000175795.2_ASM17579v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:42:16,224] [INFO] Task succeeded: Blastn
[2024-01-25 18:42:16,226] [INFO] Selected 8 target genomes.
[2024-01-25 18:42:16,227] [INFO] Target genome list was writen to GCF_000175795.2_ASM17579v2_genomic.fna/target_genomes.txt
[2024-01-25 18:42:16,230] [INFO] Task started: fastANI
[2024-01-25 18:42:16,230] [INFO] Running command: fastANI --query /var/lib/cwl/stg62e76f0a-683f-4ccb-b621-2ecd686e2eb2/GCF_000175795.2_ASM17579v2_genomic.fna.gz --refList GCF_000175795.2_ASM17579v2_genomic.fna/target_genomes.txt --output GCF_000175795.2_ASM17579v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:42:23,912] [INFO] Task succeeded: fastANI
[2024-01-25 18:42:23,913] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge99e7ab2-dbbf-405e-998a-cb4e25ff797d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:42:23,913] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge99e7ab2-dbbf-405e-998a-cb4e25ff797d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:42:23,919] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:42:23,919] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:42:23,919] [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 papyrosolvens	strain=DSM 2782	GCA_000175795.2	29362	29362	type	True	100.0	1622	1626	95	conclusive
Ruminiclostridium josui	strain=JCM 17888	GCA_001311015.1	1499	1499	type	True	86.1961	907	1626	95	below_threshold
Ruminiclostridium josui	strain=JCM 17888	GCA_000526495.1	1499	1499	type	True	86.1174	943	1626	95	below_threshold
Ruminiclostridium cellulolyticum	strain=H10; ATCC 35319	GCA_000022065.1	1521	1521	type	True	84.1786	880	1626	95	below_threshold
Ruminiclostridium hungatei	strain=DSM 14427	GCA_002051585.1	48256	48256	type	True	78.2123	205	1626	95	below_threshold
Ruminiclostridium cellobioparum	strain=ATCC 15832	GCA_000621505.1	29355	29355	type	True	78.0944	241	1626	95	below_threshold
Ruminiclostridium cellobioparum subsp. termitidis	strain=CT1112	GCA_000350485.1	29371	29355	type	True	77.607	213	1626	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:42:23,920] [INFO] DFAST Taxonomy check result was written to GCF_000175795.2_ASM17579v2_genomic.fna/tc_result.tsv
[2024-01-25 18:42:23,921] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:42:23,921] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:42:23,921] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge99e7ab2-dbbf-405e-998a-cb4e25ff797d/dqc_reference/checkm_data
[2024-01-25 18:42:23,922] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:42:23,966] [INFO] Task started: CheckM
[2024-01-25 18:42:23,967] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000175795.2_ASM17579v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000175795.2_ASM17579v2_genomic.fna/checkm_input GCF_000175795.2_ASM17579v2_genomic.fna/checkm_result
[2024-01-25 18:42:54,120] [INFO] Task succeeded: CheckM
[2024-01-25 18:42:54,122] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:42:54,140] [INFO] ===== Completeness check finished =====
[2024-01-25 18:42:54,140] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:42:54,140] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000175795.2_ASM17579v2_genomic.fna/markers.fasta)
[2024-01-25 18:42:54,141] [INFO] Task started: Blastn
[2024-01-25 18:42:54,141] [INFO] Running command: blastn -query GCF_000175795.2_ASM17579v2_genomic.fna/markers.fasta -db /var/lib/cwl/stge99e7ab2-dbbf-405e-998a-cb4e25ff797d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000175795.2_ASM17579v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:42:55,089] [INFO] Task succeeded: Blastn
[2024-01-25 18:42:55,091] [INFO] Selected 5 target genomes.
[2024-01-25 18:42:55,091] [INFO] Target genome list was writen to GCF_000175795.2_ASM17579v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:42:55,095] [INFO] Task started: fastANI
[2024-01-25 18:42:55,095] [INFO] Running command: fastANI --query /var/lib/cwl/stg62e76f0a-683f-4ccb-b621-2ecd686e2eb2/GCF_000175795.2_ASM17579v2_genomic.fna.gz --refList GCF_000175795.2_ASM17579v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000175795.2_ASM17579v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:43:00,843] [INFO] Task succeeded: fastANI
[2024-01-25 18:43:00,847] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:43:00,847] [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_000175795.2	s__Ruminiclostridium papyrosolvens	100.0	1622	1626	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_000244875.1	s__Ruminiclostridium sp000244875	89.5638	1056	1626	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	89.1841	1037	1626	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	86.1281	942	1626	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_000022065.1	s__Ruminiclostridium cellulolyticum	84.1721	880	1626	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	-
--------------------------------------------------------------------------------
[2024-01-25 18:43:00,849] [INFO] GTDB search result was written to GCF_000175795.2_ASM17579v2_genomic.fna/result_gtdb.tsv
[2024-01-25 18:43:00,849] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:43:00,851] [INFO] DFAST_QC result json was written to GCF_000175795.2_ASM17579v2_genomic.fna/dqc_result.json
[2024-01-25 18:43:00,852] [INFO] DFAST_QC completed!
[2024-01-25 18:43:00,852] [INFO] Total running time: 0h0m55s