[2023-06-27 03:49:13,425] [INFO] DFAST_QC pipeline started.
[2023-06-27 03:49:13,427] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 03:49:13,428] [INFO] DQC Reference Directory: /var/lib/cwl/stg478cedb5-623d-4978-9fd0-a1868db5e097/dqc_reference
[2023-06-27 03:49:14,746] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 03:49:14,747] [INFO] Task started: Prodigal
[2023-06-27 03:49:14,747] [INFO] Running command: gunzip -c /var/lib/cwl/stg24047657-da2b-409c-b460-dc5385c87365/GCA_002395545.1_ASM239554v1_genomic.fna.gz | prodigal -d GCA_002395545.1_ASM239554v1_genomic.fna/cds.fna -a GCA_002395545.1_ASM239554v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 03:49:19,229] [INFO] Task succeeded: Prodigal
[2023-06-27 03:49:19,230] [INFO] Task started: HMMsearch
[2023-06-27 03:49:19,230] [INFO] Running command: hmmsearch --tblout GCA_002395545.1_ASM239554v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg478cedb5-623d-4978-9fd0-a1868db5e097/dqc_reference/reference_markers.hmm GCA_002395545.1_ASM239554v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 03:49:19,494] [INFO] Task succeeded: HMMsearch
[2023-06-27 03:49:19,495] [INFO] Found 6/6 markers.
[2023-06-27 03:49:19,520] [INFO] Query marker FASTA was written to GCA_002395545.1_ASM239554v1_genomic.fna/markers.fasta
[2023-06-27 03:49:19,521] [INFO] Task started: Blastn
[2023-06-27 03:49:19,521] [INFO] Running command: blastn -query GCA_002395545.1_ASM239554v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg478cedb5-623d-4978-9fd0-a1868db5e097/dqc_reference/reference_markers.fasta -out GCA_002395545.1_ASM239554v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 03:49:20,145] [INFO] Task succeeded: Blastn
[2023-06-27 03:49:20,151] [INFO] Selected 27 target genomes.
[2023-06-27 03:49:20,152] [INFO] Target genome list was writen to GCA_002395545.1_ASM239554v1_genomic.fna/target_genomes.txt
[2023-06-27 03:49:20,157] [INFO] Task started: fastANI
[2023-06-27 03:49:20,158] [INFO] Running command: fastANI --query /var/lib/cwl/stg24047657-da2b-409c-b460-dc5385c87365/GCA_002395545.1_ASM239554v1_genomic.fna.gz --refList GCA_002395545.1_ASM239554v1_genomic.fna/target_genomes.txt --output GCA_002395545.1_ASM239554v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 03:49:32,328] [INFO] Task succeeded: fastANI
[2023-06-27 03:49:32,328] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg478cedb5-623d-4978-9fd0-a1868db5e097/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 03:49:32,329] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg478cedb5-623d-4978-9fd0-a1868db5e097/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 03:49:32,339] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 03:49:32,339] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 03:49:32,339] [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
Eubacterium ruminantium	strain=ATCC 17233	GCA_900167085.1	42322	42322	type	True	78.2229	107	697	95	below_threshold
Coprococcus eutactus	strain=ATCC 27759	GCA_025149915.1	33043	33043	suspected-type	True	76.5916	50	697	95	below_threshold
Coprococcus eutactus	strain=ATCC 27759	GCA_000154425.1	33043	33043	suspected-type	True	76.5356	51	697	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 03:49:32,341] [INFO] DFAST Taxonomy check result was written to GCA_002395545.1_ASM239554v1_genomic.fna/tc_result.tsv
[2023-06-27 03:49:32,342] [INFO] ===== Taxonomy check completed =====
[2023-06-27 03:49:32,342] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 03:49:32,342] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg478cedb5-623d-4978-9fd0-a1868db5e097/dqc_reference/checkm_data
[2023-06-27 03:49:32,343] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 03:49:32,373] [INFO] Task started: CheckM
[2023-06-27 03:49:32,373] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002395545.1_ASM239554v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002395545.1_ASM239554v1_genomic.fna/checkm_input GCA_002395545.1_ASM239554v1_genomic.fna/checkm_result
[2023-06-27 03:49:53,825] [INFO] Task succeeded: CheckM
[2023-06-27 03:49:53,826] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.93%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 03:49:53,848] [INFO] ===== Completeness check finished =====
[2023-06-27 03:49:53,848] [INFO] ===== Start GTDB Search =====
[2023-06-27 03:49:53,848] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002395545.1_ASM239554v1_genomic.fna/markers.fasta)
[2023-06-27 03:49:53,849] [INFO] Task started: Blastn
[2023-06-27 03:49:53,849] [INFO] Running command: blastn -query GCA_002395545.1_ASM239554v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg478cedb5-623d-4978-9fd0-a1868db5e097/dqc_reference/reference_markers_gtdb.fasta -out GCA_002395545.1_ASM239554v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 03:49:54,884] [INFO] Task succeeded: Blastn
[2023-06-27 03:49:54,889] [INFO] Selected 19 target genomes.
[2023-06-27 03:49:54,889] [INFO] Target genome list was writen to GCA_002395545.1_ASM239554v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 03:49:54,907] [INFO] Task started: fastANI
[2023-06-27 03:49:54,908] [INFO] Running command: fastANI --query /var/lib/cwl/stg24047657-da2b-409c-b460-dc5385c87365/GCA_002395545.1_ASM239554v1_genomic.fna.gz --refList GCA_002395545.1_ASM239554v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002395545.1_ASM239554v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 03:50:03,675] [INFO] Task succeeded: fastANI
[2023-06-27 03:50:03,699] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 03:50:03,699] [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_000687655.1	s__Eubacterium_Q sp000687655	96.9097	625	697	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_Q	95.0	96.91	96.91	0.90	0.90	2	conclusive
GCA_017477505.1	s__Eubacterium_Q sp017477505	79.9613	315	697	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_Q	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000702245.1	s__Eubacterium_Q sp000702245	78.3023	108	697	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_Q	95.0	98.40	97.61	0.92	0.88	4	-
GCA_017519155.1	s__Eubacterium_Q sp017519155	78.1967	81	697	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_Q	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108205.1	s__Eubacterium_Q ruminantium_A	78.151	117	697	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_Q	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900199595.1	s__Eubacterium_Q sp900199595	78.1272	115	697	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_Q	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017430325.1	s__Eubacterium_Q sp017430325	77.9131	115	697	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_Q	95.0	98.28	98.28	0.91	0.91	2	-
GCA_902780985.1	s__Eubacterium_Q sp902780985	77.9042	94	697	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_Q	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002350525.1	s__Eubacterium_Q sp002350525	77.4385	117	697	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_Q	95.0	98.75	97.74	0.91	0.85	4	-
GCA_902781895.1	s__Eubacterium_Q sp902781895	77.4112	93	697	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_Q	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900316715.1	s__Eubacterium_Q sp900316715	77.3431	117	697	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_Q	95.0	98.73	96.50	0.86	0.78	14	-
GCA_900321215.1	s__Eubacterium_Q sp900321215	77.3405	91	697	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_Q	95.0	99.10	98.50	0.87	0.75	5	-
GCA_902760415.1	s__Eubacterium_Q sp002349225	77.2448	94	697	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_Q	95.0	98.66	98.14	0.88	0.86	4	-
GCA_017449765.1	s__CAG-127 sp017449765	76.7545	57	697	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-127	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003482105.1	s__Coprococcus sp000433075	76.4375	53	697	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus	95.0	99.05	98.02	0.96	0.92	5	-
GCA_902772925.1	s__Eubacterium_Q sp902772925	76.2189	69	697	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_Q	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 03:50:03,701] [INFO] GTDB search result was written to GCA_002395545.1_ASM239554v1_genomic.fna/result_gtdb.tsv
[2023-06-27 03:50:03,702] [INFO] ===== GTDB Search completed =====
[2023-06-27 03:50:03,705] [INFO] DFAST_QC result json was written to GCA_002395545.1_ASM239554v1_genomic.fna/dqc_result.json
[2023-06-27 03:50:03,705] [INFO] DFAST_QC completed!
[2023-06-27 03:50:03,705] [INFO] Total running time: 0h0m50s