[2023-06-28 16:01:14,330] [INFO] DFAST_QC pipeline started.
[2023-06-28 16:01:14,333] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 16:01:14,333] [INFO] DQC Reference Directory: /var/lib/cwl/stgde29394c-8dfb-47ee-bdd2-ee60fc69d820/dqc_reference
[2023-06-28 16:01:15,571] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 16:01:15,572] [INFO] Task started: Prodigal
[2023-06-28 16:01:15,572] [INFO] Running command: gunzip -c /var/lib/cwl/stg26ec5b3a-24b3-4975-be6e-13085919e502/GCA_017521985.1_ASM1752198v1_genomic.fna.gz | prodigal -d GCA_017521985.1_ASM1752198v1_genomic.fna/cds.fna -a GCA_017521985.1_ASM1752198v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 16:01:23,471] [INFO] Task succeeded: Prodigal
[2023-06-28 16:01:23,472] [INFO] Task started: HMMsearch
[2023-06-28 16:01:23,472] [INFO] Running command: hmmsearch --tblout GCA_017521985.1_ASM1752198v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgde29394c-8dfb-47ee-bdd2-ee60fc69d820/dqc_reference/reference_markers.hmm GCA_017521985.1_ASM1752198v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 16:01:23,683] [INFO] Task succeeded: HMMsearch
[2023-06-28 16:01:23,684] [INFO] Found 6/6 markers.
[2023-06-28 16:01:23,716] [INFO] Query marker FASTA was written to GCA_017521985.1_ASM1752198v1_genomic.fna/markers.fasta
[2023-06-28 16:01:23,716] [INFO] Task started: Blastn
[2023-06-28 16:01:23,716] [INFO] Running command: blastn -query GCA_017521985.1_ASM1752198v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde29394c-8dfb-47ee-bdd2-ee60fc69d820/dqc_reference/reference_markers.fasta -out GCA_017521985.1_ASM1752198v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:01:24,333] [INFO] Task succeeded: Blastn
[2023-06-28 16:01:24,337] [INFO] Selected 33 target genomes.
[2023-06-28 16:01:24,337] [INFO] Target genome list was writen to GCA_017521985.1_ASM1752198v1_genomic.fna/target_genomes.txt
[2023-06-28 16:01:24,338] [INFO] Task started: fastANI
[2023-06-28 16:01:24,338] [INFO] Running command: fastANI --query /var/lib/cwl/stg26ec5b3a-24b3-4975-be6e-13085919e502/GCA_017521985.1_ASM1752198v1_genomic.fna.gz --refList GCA_017521985.1_ASM1752198v1_genomic.fna/target_genomes.txt --output GCA_017521985.1_ASM1752198v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 16:01:43,428] [INFO] Task succeeded: fastANI
[2023-06-28 16:01:43,429] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgde29394c-8dfb-47ee-bdd2-ee60fc69d820/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 16:01:43,429] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgde29394c-8dfb-47ee-bdd2-ee60fc69d820/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 16:01:43,432] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 16:01:43,432] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 16:01:43,432] [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
Roseburia inulinivorans	strain=DSM 16841	GCA_000174195.1	360807	360807	suspected-type	True	77.1028	51	1126	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 16:01:43,434] [INFO] DFAST Taxonomy check result was written to GCA_017521985.1_ASM1752198v1_genomic.fna/tc_result.tsv
[2023-06-28 16:01:43,435] [INFO] ===== Taxonomy check completed =====
[2023-06-28 16:01:43,435] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 16:01:43,435] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgde29394c-8dfb-47ee-bdd2-ee60fc69d820/dqc_reference/checkm_data
[2023-06-28 16:01:43,436] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 16:01:43,472] [INFO] Task started: CheckM
[2023-06-28 16:01:43,472] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017521985.1_ASM1752198v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017521985.1_ASM1752198v1_genomic.fna/checkm_input GCA_017521985.1_ASM1752198v1_genomic.fna/checkm_result
[2023-06-28 16:02:11,729] [INFO] Task succeeded: CheckM
[2023-06-28 16:02:11,730] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 16:02:11,746] [INFO] ===== Completeness check finished =====
[2023-06-28 16:02:11,746] [INFO] ===== Start GTDB Search =====
[2023-06-28 16:02:11,746] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017521985.1_ASM1752198v1_genomic.fna/markers.fasta)
[2023-06-28 16:02:11,747] [INFO] Task started: Blastn
[2023-06-28 16:02:11,747] [INFO] Running command: blastn -query GCA_017521985.1_ASM1752198v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde29394c-8dfb-47ee-bdd2-ee60fc69d820/dqc_reference/reference_markers_gtdb.fasta -out GCA_017521985.1_ASM1752198v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:02:12,763] [INFO] Task succeeded: Blastn
[2023-06-28 16:02:12,767] [INFO] Selected 23 target genomes.
[2023-06-28 16:02:12,767] [INFO] Target genome list was writen to GCA_017521985.1_ASM1752198v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 16:02:12,771] [INFO] Task started: fastANI
[2023-06-28 16:02:12,771] [INFO] Running command: fastANI --query /var/lib/cwl/stg26ec5b3a-24b3-4975-be6e-13085919e502/GCA_017521985.1_ASM1752198v1_genomic.fna.gz --refList GCA_017521985.1_ASM1752198v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017521985.1_ASM1752198v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 16:02:23,646] [INFO] Task succeeded: fastANI
[2023-06-28 16:02:23,660] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 16:02:23,661] [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_017521985.1	s__RGIG6307 sp017521985	100.0	1125	1126	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RGIG6307	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017516285.1	s__RGIG6307 sp017516285	80.7366	295	1126	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RGIG6307	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017513625.1	s__Acetatifactor sp017513625	79.5455	55	1126	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017461685.1	s__RGIG6307 sp017461685	79.5362	184	1126	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RGIG6307	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017520425.1	s__Acetatifactor sp017520425	79.185	73	1126	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017467845.1	s__Acetatifactor sp017467845	77.7694	77	1126	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017437065.1	s__RGIG3002 sp017437065	77.6428	77	1126	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RGIG3002	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017463255.1	s__RGIG4034 sp017463255	77.5383	71	1126	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RGIG4034	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017436305.1	s__RGIG3040 sp017436305	77.4863	58	1126	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RGIG3040	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017434885.1	s__CAG-95 sp017434885	77.3707	76	1126	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017623295.1	s__UBA3282 sp017623295	77.3171	66	1126	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015056865.1	s__SIG332 sp015056865	77.1865	57	1126	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__SIG332	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017453065.1	s__SIG332 sp017453065	76.8005	63	1126	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__SIG332	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900551115.1	s__CAG-510 sp900551115	76.7271	63	1126	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-510	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017461775.1	s__Acetatifactor sp017461775	76.6887	66	1126	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017468395.1	s__SIG332 sp017468395	76.4528	71	1126	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__SIG332	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017521195.1	s__SFDP01 sp017521195	76.2524	54	1126	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__SFDP01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 16:02:23,666] [INFO] GTDB search result was written to GCA_017521985.1_ASM1752198v1_genomic.fna/result_gtdb.tsv
[2023-06-28 16:02:23,667] [INFO] ===== GTDB Search completed =====
[2023-06-28 16:02:23,672] [INFO] DFAST_QC result json was written to GCA_017521985.1_ASM1752198v1_genomic.fna/dqc_result.json
[2023-06-28 16:02:23,672] [INFO] DFAST_QC completed!
[2023-06-28 16:02:23,672] [INFO] Total running time: 0h1m9s