[2024-01-24 11:34:39,269] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:39,271] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:39,271] [INFO] DQC Reference Directory: /var/lib/cwl/stg910c6592-c5a4-42b4-8b9e-b0f9aed468bf/dqc_reference
[2024-01-24 11:34:40,494] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:40,494] [INFO] Task started: Prodigal
[2024-01-24 11:34:40,495] [INFO] Running command: gunzip -c /var/lib/cwl/stg30d2bbb6-fdae-4aef-ae67-9cbb91fee463/GCF_014337195.1_ASM1433719v1_genomic.fna.gz | prodigal -d GCF_014337195.1_ASM1433719v1_genomic.fna/cds.fna -a GCF_014337195.1_ASM1433719v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:34:48,775] [INFO] Task succeeded: Prodigal
[2024-01-24 11:34:48,776] [INFO] Task started: HMMsearch
[2024-01-24 11:34:48,776] [INFO] Running command: hmmsearch --tblout GCF_014337195.1_ASM1433719v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg910c6592-c5a4-42b4-8b9e-b0f9aed468bf/dqc_reference/reference_markers.hmm GCF_014337195.1_ASM1433719v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:34:49,085] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:34:49,086] [INFO] Found 6/6 markers.
[2024-01-24 11:34:49,110] [INFO] Query marker FASTA was written to GCF_014337195.1_ASM1433719v1_genomic.fna/markers.fasta
[2024-01-24 11:34:49,111] [INFO] Task started: Blastn
[2024-01-24 11:34:49,111] [INFO] Running command: blastn -query GCF_014337195.1_ASM1433719v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg910c6592-c5a4-42b4-8b9e-b0f9aed468bf/dqc_reference/reference_markers.fasta -out GCF_014337195.1_ASM1433719v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:34:49,702] [INFO] Task succeeded: Blastn
[2024-01-24 11:34:49,705] [INFO] Selected 23 target genomes.
[2024-01-24 11:34:49,706] [INFO] Target genome list was writen to GCF_014337195.1_ASM1433719v1_genomic.fna/target_genomes.txt
[2024-01-24 11:34:49,713] [INFO] Task started: fastANI
[2024-01-24 11:34:49,713] [INFO] Running command: fastANI --query /var/lib/cwl/stg30d2bbb6-fdae-4aef-ae67-9cbb91fee463/GCF_014337195.1_ASM1433719v1_genomic.fna.gz --refList GCF_014337195.1_ASM1433719v1_genomic.fna/target_genomes.txt --output GCF_014337195.1_ASM1433719v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:06,402] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:06,402] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg910c6592-c5a4-42b4-8b9e-b0f9aed468bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:06,402] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg910c6592-c5a4-42b4-8b9e-b0f9aed468bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:06,411] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:06,411] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:06,411] [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
Qiania dongpingensis	strain=NSJ-38	GCA_014337195.1	2763669	2763669	type	True	100.0	1027	1028	95	conclusive
Eisenbergiella porci	strain=WCA-389-WT-23B	GCA_009696275.1	2652274	2652274	type	True	79.3964	67	1028	95	below_threshold
Ruminococcus gauvreauii	strain=DSM 19829	GCA_025151995.1	438033	438033	type	True	78.9533	60	1028	95	below_threshold
Enterocloster clostridioformis	strain=NCTC11224	GCA_900447015.1	1531	1531	suspected-type	True	78.2794	62	1028	95	below_threshold
Enterocloster clostridioformis	strain=FDAARGOS_1529	GCA_020297485.1	1531	1531	suspected-type	True	78.2587	63	1028	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_001689125.2	1796616	1796616	type	True	78.2466	53	1028	95	below_threshold
Ruminococcus gauvreauii	strain=DSM 19829	GCA_000425525.1	438033	438033	type	True	77.8428	61	1028	95	below_threshold
Diplocloster agilis	strain=ASD5720	GCA_019042275.1	2850323	2850323	type	True	77.1763	56	1028	95	below_threshold
Enterocloster clostridioformis	strain=ATCC 25537	GCA_900113155.1	1531	1531	type	True	77.095	62	1028	95	below_threshold
Cuneatibacter caecimuris	strain=DSM 29486	GCA_004216775.1	1796618	1796618	type	True	76.7321	63	1028	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:06,413] [INFO] DFAST Taxonomy check result was written to GCF_014337195.1_ASM1433719v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:06,414] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:06,414] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:06,414] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg910c6592-c5a4-42b4-8b9e-b0f9aed468bf/dqc_reference/checkm_data
[2024-01-24 11:35:06,415] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:06,449] [INFO] Task started: CheckM
[2024-01-24 11:35:06,449] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014337195.1_ASM1433719v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014337195.1_ASM1433719v1_genomic.fna/checkm_input GCF_014337195.1_ASM1433719v1_genomic.fna/checkm_result
[2024-01-24 11:35:35,789] [INFO] Task succeeded: CheckM
[2024-01-24 11:35:35,790] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:35:35,806] [INFO] ===== Completeness check finished =====
[2024-01-24 11:35:35,807] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:35:35,807] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014337195.1_ASM1433719v1_genomic.fna/markers.fasta)
[2024-01-24 11:35:35,807] [INFO] Task started: Blastn
[2024-01-24 11:35:35,807] [INFO] Running command: blastn -query GCF_014337195.1_ASM1433719v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg910c6592-c5a4-42b4-8b9e-b0f9aed468bf/dqc_reference/reference_markers_gtdb.fasta -out GCF_014337195.1_ASM1433719v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:36,706] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:36,710] [INFO] Selected 14 target genomes.
[2024-01-24 11:35:36,710] [INFO] Target genome list was writen to GCF_014337195.1_ASM1433719v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:35:36,753] [INFO] Task started: fastANI
[2024-01-24 11:35:36,753] [INFO] Running command: fastANI --query /var/lib/cwl/stg30d2bbb6-fdae-4aef-ae67-9cbb91fee463/GCF_014337195.1_ASM1433719v1_genomic.fna.gz --refList GCF_014337195.1_ASM1433719v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014337195.1_ASM1433719v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:35:46,732] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:46,739] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:35:46,740] [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
GCA_014337195.1	s__Paralachnospira sp014337195	100.0	1027	1028	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Paralachnospira	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902363445.1	s__Paralachnospira sp902363445	93.2378	879	1028	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Paralachnospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904379015.1	s__Paralachnospira caecorum	78.4081	262	1028	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Paralachnospira	95.0	99.98	99.98	0.92	0.92	2	-
GCF_904420245.1	s__Paralachnospira avium	77.5082	226	1028	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Paralachnospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587905.1	s__Paralachnospira sp910587905	77.2355	158	1028	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Paralachnospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588815.1	s__Paralachnospira sp910588815	77.2068	195	1028	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Paralachnospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000466485.1	s__Clostridium_Q symbiosum	76.6193	52	1028	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_Q	95.0	98.86	98.57	0.86	0.81	32	-
GCA_910575565.1	s__Caccovicinus sp910575565	76.5919	60	1028	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Caccovicinus	95.0	99.12	99.12	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:35:46,741] [INFO] GTDB search result was written to GCF_014337195.1_ASM1433719v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:35:46,742] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:35:46,745] [INFO] DFAST_QC result json was written to GCF_014337195.1_ASM1433719v1_genomic.fna/dqc_result.json
[2024-01-24 11:35:46,745] [INFO] DFAST_QC completed!
[2024-01-24 11:35:46,745] [INFO] Total running time: 0h1m7s