[2024-01-25 17:53:51,479] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:53:51,480] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:53:51,480] [INFO] DQC Reference Directory: /var/lib/cwl/stg9fdaf431-5419-4217-ad0a-f0ffbdd6aefb/dqc_reference
[2024-01-25 17:53:52,617] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:53:52,618] [INFO] Task started: Prodigal
[2024-01-25 17:53:52,618] [INFO] Running command: gunzip -c /var/lib/cwl/stg515649c5-1e0f-4df9-a7d5-fa57e48f84e0/GCF_005121165.3_ASM512116v3_genomic.fna.gz | prodigal -d GCF_005121165.3_ASM512116v3_genomic.fna/cds.fna -a GCF_005121165.3_ASM512116v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:54:02,399] [INFO] Task succeeded: Prodigal
[2024-01-25 17:54:02,399] [INFO] Task started: HMMsearch
[2024-01-25 17:54:02,399] [INFO] Running command: hmmsearch --tblout GCF_005121165.3_ASM512116v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9fdaf431-5419-4217-ad0a-f0ffbdd6aefb/dqc_reference/reference_markers.hmm GCF_005121165.3_ASM512116v3_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:54:02,619] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:54:02,621] [INFO] Found 6/6 markers.
[2024-01-25 17:54:02,656] [INFO] Query marker FASTA was written to GCF_005121165.3_ASM512116v3_genomic.fna/markers.fasta
[2024-01-25 17:54:02,656] [INFO] Task started: Blastn
[2024-01-25 17:54:02,657] [INFO] Running command: blastn -query GCF_005121165.3_ASM512116v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg9fdaf431-5419-4217-ad0a-f0ffbdd6aefb/dqc_reference/reference_markers.fasta -out GCF_005121165.3_ASM512116v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:54:03,306] [INFO] Task succeeded: Blastn
[2024-01-25 17:54:03,309] [INFO] Selected 13 target genomes.
[2024-01-25 17:54:03,309] [INFO] Target genome list was writen to GCF_005121165.3_ASM512116v3_genomic.fna/target_genomes.txt
[2024-01-25 17:54:03,324] [INFO] Task started: fastANI
[2024-01-25 17:54:03,324] [INFO] Running command: fastANI --query /var/lib/cwl/stg515649c5-1e0f-4df9-a7d5-fa57e48f84e0/GCF_005121165.3_ASM512116v3_genomic.fna.gz --refList GCF_005121165.3_ASM512116v3_genomic.fna/target_genomes.txt --output GCF_005121165.3_ASM512116v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:54:10,605] [INFO] Task succeeded: fastANI
[2024-01-25 17:54:10,606] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9fdaf431-5419-4217-ad0a-f0ffbdd6aefb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:54:10,606] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9fdaf431-5419-4217-ad0a-f0ffbdd6aefb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:54:10,614] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:54:10,615] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:54:10,615] [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
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	100.0	1191	1192	95	conclusive
Faecalibacterium duncaniae	strain=A2-165	GCA_000162015.1	411483	411483	type	True	81.1001	106	1192	95	below_threshold
Faecalibacterium duncaniae	strain=JCM 31915	GCA_010509575.1	411483	411483	type	True	81.0837	113	1192	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	80.7776	292	1192	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	80.6197	265	1192	95	below_threshold
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	80.607	220	1192	95	below_threshold
Pusillibacter faecalis	strain=MM59	GCA_018408705.1	2714358	2714358	type	True	80.4289	376	1192	95	below_threshold
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	80.2413	273	1192	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	79.6632	324	1192	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	79.6007	244	1192	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	78.8222	240	1192	95	below_threshold
Oscillibacter ruminantium	strain=GH1	GCA_000307265.1	1263547	1263547	type	True	78.3665	267	1192	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:54:10,616] [INFO] DFAST Taxonomy check result was written to GCF_005121165.3_ASM512116v3_genomic.fna/tc_result.tsv
[2024-01-25 17:54:10,617] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:54:10,617] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:54:10,617] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9fdaf431-5419-4217-ad0a-f0ffbdd6aefb/dqc_reference/checkm_data
[2024-01-25 17:54:10,618] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:54:10,656] [INFO] Task started: CheckM
[2024-01-25 17:54:10,656] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005121165.3_ASM512116v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005121165.3_ASM512116v3_genomic.fna/checkm_input GCF_005121165.3_ASM512116v3_genomic.fna/checkm_result
[2024-01-25 17:54:41,111] [INFO] Task succeeded: CheckM
[2024-01-25 17:54:41,112] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:54:41,132] [INFO] ===== Completeness check finished =====
[2024-01-25 17:54:41,132] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:54:41,132] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005121165.3_ASM512116v3_genomic.fna/markers.fasta)
[2024-01-25 17:54:41,132] [INFO] Task started: Blastn
[2024-01-25 17:54:41,133] [INFO] Running command: blastn -query GCF_005121165.3_ASM512116v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg9fdaf431-5419-4217-ad0a-f0ffbdd6aefb/dqc_reference/reference_markers_gtdb.fasta -out GCF_005121165.3_ASM512116v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:54:42,477] [INFO] Task succeeded: Blastn
[2024-01-25 17:54:42,488] [INFO] Selected 8 target genomes.
[2024-01-25 17:54:42,488] [INFO] Target genome list was writen to GCF_005121165.3_ASM512116v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:54:42,499] [INFO] Task started: fastANI
[2024-01-25 17:54:42,500] [INFO] Running command: fastANI --query /var/lib/cwl/stg515649c5-1e0f-4df9-a7d5-fa57e48f84e0/GCF_005121165.3_ASM512116v3_genomic.fna.gz --refList GCF_005121165.3_ASM512116v3_genomic.fna/target_genomes_gtdb.txt --output GCF_005121165.3_ASM512116v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:54:48,003] [INFO] Task succeeded: fastANI
[2024-01-25 17:54:48,010] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:54:48,010] [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_005121165.2	s__Dysosmobacter welbionis	99.9999	1191	1192	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	98.82	98.27	0.84	0.73	10	conclusive
GCA_019118935.1	s__Dysosmobacter pullicola	93.964	653	1192	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	98.04	97.82	0.81	0.80	3	-
GCA_019118245.1	s__Dysosmobacter excrementigallinarum	88.6314	587	1192	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019118505.1	s__Dysosmobacter excrementavium	88.4961	559	1192	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016902445.1	s__Dysosmobacter avistercoris	88.1401	669	1192	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	98.12	97.84	0.91	0.85	7	-
GCF_018228705.1	s__Dysosmobacter sp018228705	83.8795	594	1192	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900770295.1	s__Dysosmobacter sp900770295	82.5589	462	1192	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:54:48,011] [INFO] GTDB search result was written to GCF_005121165.3_ASM512116v3_genomic.fna/result_gtdb.tsv
[2024-01-25 17:54:48,012] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:54:48,015] [INFO] DFAST_QC result json was written to GCF_005121165.3_ASM512116v3_genomic.fna/dqc_result.json
[2024-01-25 17:54:48,015] [INFO] DFAST_QC completed!
[2024-01-25 17:54:48,015] [INFO] Total running time: 0h0m57s