[2023-07-01 04:51:11,388] [INFO] DFAST_QC pipeline started.
[2023-07-01 04:51:11,398] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 04:51:11,398] [INFO] DQC Reference Directory: /var/lib/cwl/stg40c088ec-31db-4e45-8ca4-673be713a387/dqc_reference
[2023-07-01 04:51:14,260] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 04:51:14,262] [INFO] Task started: Prodigal
[2023-07-01 04:51:14,262] [INFO] Running command: gunzip -c /var/lib/cwl/stg22957c8a-91b8-4a10-a57b-36207aea3aa3/GCA_024697705.1_ASM2469770v1_genomic.fna.gz | prodigal -d GCA_024697705.1_ASM2469770v1_genomic.fna/cds.fna -a GCA_024697705.1_ASM2469770v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 04:51:20,727] [INFO] Task succeeded: Prodigal
[2023-07-01 04:51:20,727] [INFO] Task started: HMMsearch
[2023-07-01 04:51:20,727] [INFO] Running command: hmmsearch --tblout GCA_024697705.1_ASM2469770v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg40c088ec-31db-4e45-8ca4-673be713a387/dqc_reference/reference_markers.hmm GCA_024697705.1_ASM2469770v1_genomic.fna/protein.faa > /dev/null
[2023-07-01 04:51:21,033] [INFO] Task succeeded: HMMsearch
[2023-07-01 04:51:21,034] [INFO] Found 6/6 markers.
[2023-07-01 04:51:21,072] [INFO] Query marker FASTA was written to GCA_024697705.1_ASM2469770v1_genomic.fna/markers.fasta
[2023-07-01 04:51:21,073] [INFO] Task started: Blastn
[2023-07-01 04:51:21,073] [INFO] Running command: blastn -query GCA_024697705.1_ASM2469770v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg40c088ec-31db-4e45-8ca4-673be713a387/dqc_reference/reference_markers.fasta -out GCA_024697705.1_ASM2469770v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 04:51:21,727] [INFO] Task succeeded: Blastn
[2023-07-01 04:51:21,731] [INFO] Selected 22 target genomes.
[2023-07-01 04:51:21,731] [INFO] Target genome list was writen to GCA_024697705.1_ASM2469770v1_genomic.fna/target_genomes.txt
[2023-07-01 04:51:21,736] [INFO] Task started: fastANI
[2023-07-01 04:51:21,736] [INFO] Running command: fastANI --query /var/lib/cwl/stg22957c8a-91b8-4a10-a57b-36207aea3aa3/GCA_024697705.1_ASM2469770v1_genomic.fna.gz --refList GCA_024697705.1_ASM2469770v1_genomic.fna/target_genomes.txt --output GCA_024697705.1_ASM2469770v1_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 04:51:36,628] [INFO] Task succeeded: fastANI
[2023-07-01 04:51:36,628] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg40c088ec-31db-4e45-8ca4-673be713a387/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 04:51:36,628] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg40c088ec-31db-4e45-8ca4-673be713a387/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 04:51:36,634] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 04:51:36,634] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-07-01 04:51:36,634] [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
Ruminococcus albus	strain=DSM 20455	GCA_000621285.1	1264	1264	suspected-type	True	77.7444	93	882	95	below_threshold
Ruminococcus albus	strain=7	GCA_000179635.2	1264	1264	suspected-type	True	77.6952	93	882	95	below_threshold
Ruminococcus flavefaciens	strain=ATCC 19208	GCA_000518765.1	1265	1265	suspected-type	True	76.3214	52	882	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 04:51:36,638] [INFO] DFAST Taxonomy check result was written to GCA_024697705.1_ASM2469770v1_genomic.fna/tc_result.tsv
[2023-07-01 04:51:36,639] [INFO] ===== Taxonomy check completed =====
[2023-07-01 04:51:36,639] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 04:51:36,640] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg40c088ec-31db-4e45-8ca4-673be713a387/dqc_reference/checkm_data
[2023-07-01 04:51:36,641] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 04:51:36,674] [INFO] Task started: CheckM
[2023-07-01 04:51:36,674] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024697705.1_ASM2469770v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024697705.1_ASM2469770v1_genomic.fna/checkm_input GCA_024697705.1_ASM2469770v1_genomic.fna/checkm_result
[2023-07-01 04:52:02,695] [INFO] Task succeeded: CheckM
[2023-07-01 04:52:02,696] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 04:52:02,717] [INFO] ===== Completeness check finished =====
[2023-07-01 04:52:02,717] [INFO] ===== Start GTDB Search =====
[2023-07-01 04:52:02,718] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024697705.1_ASM2469770v1_genomic.fna/markers.fasta)
[2023-07-01 04:52:02,718] [INFO] Task started: Blastn
[2023-07-01 04:52:02,718] [INFO] Running command: blastn -query GCA_024697705.1_ASM2469770v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg40c088ec-31db-4e45-8ca4-673be713a387/dqc_reference/reference_markers_gtdb.fasta -out GCA_024697705.1_ASM2469770v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 04:52:03,833] [INFO] Task succeeded: Blastn
[2023-07-01 04:52:03,838] [INFO] Selected 13 target genomes.
[2023-07-01 04:52:03,839] [INFO] Target genome list was writen to GCA_024697705.1_ASM2469770v1_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 04:52:03,849] [INFO] Task started: fastANI
[2023-07-01 04:52:03,849] [INFO] Running command: fastANI --query /var/lib/cwl/stg22957c8a-91b8-4a10-a57b-36207aea3aa3/GCA_024697705.1_ASM2469770v1_genomic.fna.gz --refList GCA_024697705.1_ASM2469770v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024697705.1_ASM2469770v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 04:52:11,105] [INFO] Task succeeded: fastANI
[2023-07-01 04:52:11,117] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-07-01 04:52:11,118] [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_902776945.1	s__Ruminococcus_D sp902776945	87.4128	687	882	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902781565.1	s__Ruminococcus_D sp902781565	79.3031	321	882	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900119155.1	s__Ruminococcus_D sp900119155	78.5518	292	882	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	99.98	99.98	0.99	0.99	2	-
GCA_902766335.1	s__Ruminococcus_D sp902766335	77.9284	193	882	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000434695.1	s__Ruminococcus_D sp000434695	77.5784	143	882	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	98.00	97.86	0.87	0.86	4	-
GCA_902797535.1	s__Ruminococcus_D sp902797535	77.2034	115	882	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	97.84	97.84	0.78	0.78	2	-
GCA_900104495.1	s__Ruminococcus_D sp900104495	77.1942	118	882	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017450925.1	s__Ruminococcus_D sp017450925	76.927	64	882	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017478965.1	s__Ruminococcus_D sp017478965	76.8734	58	882	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902786965.1	s__Ruminococcus_D sp902786965	76.2607	78	882	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	97.48	97.28	0.83	0.79	5	-
--------------------------------------------------------------------------------
[2023-07-01 04:52:11,130] [INFO] GTDB search result was written to GCA_024697705.1_ASM2469770v1_genomic.fna/result_gtdb.tsv
[2023-07-01 04:52:11,131] [INFO] ===== GTDB Search completed =====
[2023-07-01 04:52:11,135] [INFO] DFAST_QC result json was written to GCA_024697705.1_ASM2469770v1_genomic.fna/dqc_result.json
[2023-07-01 04:52:11,135] [INFO] DFAST_QC completed!
[2023-07-01 04:52:11,136] [INFO] Total running time: 0h0m60s