[2023-06-28 06:39:49,623] [INFO] DFAST_QC pipeline started.
[2023-06-28 06:39:49,626] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 06:39:49,626] [INFO] DQC Reference Directory: /var/lib/cwl/stg10c34748-a853-4989-bd5e-5417859ed6b6/dqc_reference
[2023-06-28 06:39:53,875] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 06:39:53,877] [INFO] Task started: Prodigal
[2023-06-28 06:39:53,877] [INFO] Running command: gunzip -c /var/lib/cwl/stg374ef562-8d5d-440b-a88c-7c7bb28dc93b/GCA_017463545.1_ASM1746354v1_genomic.fna.gz | prodigal -d GCA_017463545.1_ASM1746354v1_genomic.fna/cds.fna -a GCA_017463545.1_ASM1746354v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 06:39:57,675] [INFO] Task succeeded: Prodigal
[2023-06-28 06:39:57,675] [INFO] Task started: HMMsearch
[2023-06-28 06:39:57,675] [INFO] Running command: hmmsearch --tblout GCA_017463545.1_ASM1746354v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg10c34748-a853-4989-bd5e-5417859ed6b6/dqc_reference/reference_markers.hmm GCA_017463545.1_ASM1746354v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 06:39:57,936] [INFO] Task succeeded: HMMsearch
[2023-06-28 06:39:57,938] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg374ef562-8d5d-440b-a88c-7c7bb28dc93b/GCA_017463545.1_ASM1746354v1_genomic.fna.gz]
[2023-06-28 06:39:57,964] [INFO] Query marker FASTA was written to GCA_017463545.1_ASM1746354v1_genomic.fna/markers.fasta
[2023-06-28 06:39:57,964] [INFO] Task started: Blastn
[2023-06-28 06:39:57,964] [INFO] Running command: blastn -query GCA_017463545.1_ASM1746354v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg10c34748-a853-4989-bd5e-5417859ed6b6/dqc_reference/reference_markers.fasta -out GCA_017463545.1_ASM1746354v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 06:40:01,697] [INFO] Task succeeded: Blastn
[2023-06-28 06:40:01,703] [INFO] Selected 19 target genomes.
[2023-06-28 06:40:01,704] [INFO] Target genome list was writen to GCA_017463545.1_ASM1746354v1_genomic.fna/target_genomes.txt
[2023-06-28 06:40:01,709] [INFO] Task started: fastANI
[2023-06-28 06:40:01,709] [INFO] Running command: fastANI --query /var/lib/cwl/stg374ef562-8d5d-440b-a88c-7c7bb28dc93b/GCA_017463545.1_ASM1746354v1_genomic.fna.gz --refList GCA_017463545.1_ASM1746354v1_genomic.fna/target_genomes.txt --output GCA_017463545.1_ASM1746354v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 06:40:10,993] [INFO] Task succeeded: fastANI
[2023-06-28 06:40:10,994] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg10c34748-a853-4989-bd5e-5417859ed6b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 06:40:10,995] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg10c34748-a853-4989-bd5e-5417859ed6b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 06:40:11,008] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 06:40:11,008] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 06:40:11,008] [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
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	77.1526	65	434	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	77.0752	52	434	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	76.6459	72	434	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	76.5922	69	434	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	76.5743	51	434	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 06:40:11,011] [INFO] DFAST Taxonomy check result was written to GCA_017463545.1_ASM1746354v1_genomic.fna/tc_result.tsv
[2023-06-28 06:40:11,011] [INFO] ===== Taxonomy check completed =====
[2023-06-28 06:40:11,011] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 06:40:11,012] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg10c34748-a853-4989-bd5e-5417859ed6b6/dqc_reference/checkm_data
[2023-06-28 06:40:11,013] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 06:40:11,035] [INFO] Task started: CheckM
[2023-06-28 06:40:11,036] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017463545.1_ASM1746354v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017463545.1_ASM1746354v1_genomic.fna/checkm_input GCA_017463545.1_ASM1746354v1_genomic.fna/checkm_result
[2023-06-28 06:40:30,184] [INFO] Task succeeded: CheckM
[2023-06-28 06:40:30,186] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 57.18%
Contamintation: 11.81%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-06-28 06:40:30,214] [INFO] ===== Completeness check finished =====
[2023-06-28 06:40:30,215] [INFO] ===== Start GTDB Search =====
[2023-06-28 06:40:30,215] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017463545.1_ASM1746354v1_genomic.fna/markers.fasta)
[2023-06-28 06:40:30,216] [INFO] Task started: Blastn
[2023-06-28 06:40:30,216] [INFO] Running command: blastn -query GCA_017463545.1_ASM1746354v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg10c34748-a853-4989-bd5e-5417859ed6b6/dqc_reference/reference_markers_gtdb.fasta -out GCA_017463545.1_ASM1746354v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 06:40:31,239] [INFO] Task succeeded: Blastn
[2023-06-28 06:40:31,245] [INFO] Selected 15 target genomes.
[2023-06-28 06:40:31,245] [INFO] Target genome list was writen to GCA_017463545.1_ASM1746354v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 06:40:31,252] [INFO] Task started: fastANI
[2023-06-28 06:40:31,252] [INFO] Running command: fastANI --query /var/lib/cwl/stg374ef562-8d5d-440b-a88c-7c7bb28dc93b/GCA_017463545.1_ASM1746354v1_genomic.fna.gz --refList GCA_017463545.1_ASM1746354v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017463545.1_ASM1746354v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 06:40:38,751] [INFO] Task succeeded: fastANI
[2023-06-28 06:40:38,764] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 06:40:38,765] [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_017465745.1	s__Faecousia sp017465745	83.7537	287	434	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017473225.1	s__Faecousia sp017473225	82.487	207	434	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017622295.1	s__Faecousia sp017622295	82.1436	245	434	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017516785.1	s__Faecousia sp017516785	81.4747	216	434	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017461445.1	s__Faecousia sp017461445	80.5749	215	434	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017620525.1	s__Faecousia sp017620525	80.5515	134	434	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017398105.1	s__Faecousia sp017398105	80.4869	192	434	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004562395.1	s__Faecousia sp004562395	80.4598	178	434	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015067615.1	s__Faecousia sp015067615	80.2474	206	434	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017501695.1	s__Faecousia sp017501695	80.1272	148	434	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017436785.1	s__Faecousia sp017436785	79.7655	184	434	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017409205.1	s__Faecousia sp017409205	79.7379	177	434	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004555705.1	s__Faecousia sp004555705	79.3465	170	434	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002436765.1	s__Faecousia sp002436765	79.3384	165	434	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	99.53	99.53	0.91	0.91	2	-
GCA_900544945.1	s__Faecousia sp900544945	79.2298	142	434	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	96.60	96.52	0.82	0.81	4	-
--------------------------------------------------------------------------------
[2023-06-28 06:40:38,766] [INFO] GTDB search result was written to GCA_017463545.1_ASM1746354v1_genomic.fna/result_gtdb.tsv
[2023-06-28 06:40:38,768] [INFO] ===== GTDB Search completed =====
[2023-06-28 06:40:38,771] [INFO] DFAST_QC result json was written to GCA_017463545.1_ASM1746354v1_genomic.fna/dqc_result.json
[2023-06-28 06:40:38,771] [INFO] DFAST_QC completed!
[2023-06-28 06:40:38,771] [INFO] Total running time: 0h0m49s