[2023-06-29 14:39:48,524] [INFO] DFAST_QC pipeline started.
[2023-06-29 14:39:48,526] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 14:39:48,527] [INFO] DQC Reference Directory: /var/lib/cwl/stgfaf4d11e-a2ed-4292-85fe-a03d69284ddf/dqc_reference
[2023-06-29 14:39:49,688] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 14:39:49,688] [INFO] Task started: Prodigal
[2023-06-29 14:39:49,689] [INFO] Running command: gunzip -c /var/lib/cwl/stg6e9ca6ca-ce66-425e-8876-5f3b5936918a/GCA_023401435.1_ASM2340143v1_genomic.fna.gz | prodigal -d GCA_023401435.1_ASM2340143v1_genomic.fna/cds.fna -a GCA_023401435.1_ASM2340143v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 14:39:54,410] [INFO] Task succeeded: Prodigal
[2023-06-29 14:39:54,410] [INFO] Task started: HMMsearch
[2023-06-29 14:39:54,410] [INFO] Running command: hmmsearch --tblout GCA_023401435.1_ASM2340143v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfaf4d11e-a2ed-4292-85fe-a03d69284ddf/dqc_reference/reference_markers.hmm GCA_023401435.1_ASM2340143v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 14:39:54,608] [INFO] Task succeeded: HMMsearch
[2023-06-29 14:39:54,609] [INFO] Found 6/6 markers.
[2023-06-29 14:39:54,632] [INFO] Query marker FASTA was written to GCA_023401435.1_ASM2340143v1_genomic.fna/markers.fasta
[2023-06-29 14:39:54,632] [INFO] Task started: Blastn
[2023-06-29 14:39:54,632] [INFO] Running command: blastn -query GCA_023401435.1_ASM2340143v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfaf4d11e-a2ed-4292-85fe-a03d69284ddf/dqc_reference/reference_markers.fasta -out GCA_023401435.1_ASM2340143v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:39:55,229] [INFO] Task succeeded: Blastn
[2023-06-29 14:39:55,233] [INFO] Selected 19 target genomes.
[2023-06-29 14:39:55,233] [INFO] Target genome list was writen to GCA_023401435.1_ASM2340143v1_genomic.fna/target_genomes.txt
[2023-06-29 14:39:55,238] [INFO] Task started: fastANI
[2023-06-29 14:39:55,238] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e9ca6ca-ce66-425e-8876-5f3b5936918a/GCA_023401435.1_ASM2340143v1_genomic.fna.gz --refList GCA_023401435.1_ASM2340143v1_genomic.fna/target_genomes.txt --output GCA_023401435.1_ASM2340143v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 14:40:06,565] [INFO] Task succeeded: fastANI
[2023-06-29 14:40:06,566] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfaf4d11e-a2ed-4292-85fe-a03d69284ddf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 14:40:06,566] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfaf4d11e-a2ed-4292-85fe-a03d69284ddf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 14:40:06,573] [INFO] Found 4 fastANI hits (2 hits with ANI > threshold)
[2023-06-29 14:40:06,573] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-29 14:40:06,573] [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
Butyrivibrio crossotus	strain=DSM 2876	GCA_025148445.1	45851	45851	type	True	98.6619	642	752	95	conclusive
Butyrivibrio crossotus	strain=DSM 2876	GCA_000156015.1	45851	45851	type	True	98.5998	641	752	95	conclusive
Roseburia inulinivorans	strain=DSM 16841	GCA_000174195.1	360807	360807	suspected-type	True	80.2554	50	752	95	below_threshold
Jutongia hominis	strain=BX3	GCA_014384965.1	2763664	2763664	type	True	80.0757	53	752	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 14:40:06,576] [INFO] DFAST Taxonomy check result was written to GCA_023401435.1_ASM2340143v1_genomic.fna/tc_result.tsv
[2023-06-29 14:40:06,577] [INFO] ===== Taxonomy check completed =====
[2023-06-29 14:40:06,577] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 14:40:06,577] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfaf4d11e-a2ed-4292-85fe-a03d69284ddf/dqc_reference/checkm_data
[2023-06-29 14:40:06,579] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 14:40:06,606] [INFO] Task started: CheckM
[2023-06-29 14:40:06,606] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_023401435.1_ASM2340143v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_023401435.1_ASM2340143v1_genomic.fna/checkm_input GCA_023401435.1_ASM2340143v1_genomic.fna/checkm_result
[2023-06-29 14:40:27,331] [INFO] Task succeeded: CheckM
[2023-06-29 14:40:27,332] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 6.25%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-29 14:40:27,351] [INFO] ===== Completeness check finished =====
[2023-06-29 14:40:27,351] [INFO] ===== Start GTDB Search =====
[2023-06-29 14:40:27,351] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_023401435.1_ASM2340143v1_genomic.fna/markers.fasta)
[2023-06-29 14:40:27,352] [INFO] Task started: Blastn
[2023-06-29 14:40:27,352] [INFO] Running command: blastn -query GCA_023401435.1_ASM2340143v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfaf4d11e-a2ed-4292-85fe-a03d69284ddf/dqc_reference/reference_markers_gtdb.fasta -out GCA_023401435.1_ASM2340143v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:40:28,335] [INFO] Task succeeded: Blastn
[2023-06-29 14:40:28,339] [INFO] Selected 22 target genomes.
[2023-06-29 14:40:28,339] [INFO] Target genome list was writen to GCA_023401435.1_ASM2340143v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 14:40:28,413] [INFO] Task started: fastANI
[2023-06-29 14:40:28,414] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e9ca6ca-ce66-425e-8876-5f3b5936918a/GCA_023401435.1_ASM2340143v1_genomic.fna.gz --refList GCA_023401435.1_ASM2340143v1_genomic.fna/target_genomes_gtdb.txt --output GCA_023401435.1_ASM2340143v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 14:40:39,103] [INFO] Task succeeded: fastANI
[2023-06-29 14:40:39,113] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 14:40:39,114] [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
GCF_000156015.1	s__Butyrivibrio_A crossotus	98.5998	641	752	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio_A	95.0	98.48	97.83	0.85	0.60	12	conclusive
GCF_014287955.1	s__Lachnospira sp900316325	78.2537	105	752	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	98.86	98.35	0.93	0.88	10	-
GCF_003464165.1	s__Lachnospira sp003451515	77.9874	81	752	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	97.95	97.44	0.88	0.84	9	-
GCA_000431815.1	s__Butyrivibrio_A sp000431815	77.9319	140	752	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio_A	95.0	98.85	98.85	0.94	0.94	3	-
GCA_900768755.1	s__Butyrivibrio_A sp900768755	77.8662	68	752	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016297265.1	s__Butyrivibrio_A sp016297265	77.8085	103	752	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyrivibrio_A	95.0	98.79	98.79	0.89	0.89	2	-
GCF_018918265.1	s__Falcatimonas sp018918265	77.7197	100	752	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Falcatimonas	95.0	98.30	98.30	0.93	0.93	2	-
GCF_003458705.1	s__Lachnospira sp003537285	77.678	90	752	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.4867	98.01	96.87	0.87	0.80	8	-
GCA_900545175.1	s__CAG-882 sp900545175	77.5142	66	752	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-882	95.0	99.03	98.05	0.94	0.87	3	-
GCA_002351535.1	s__UBA2821 sp002351535	76.9514	69	752	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA2821	95.0	99.98	99.98	0.97	0.97	2	-
GCA_900551945.1	s__Lachnospira sp900551945	76.0	53	752	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	99.31	99.16	0.89	0.87	3	-
--------------------------------------------------------------------------------
[2023-06-29 14:40:39,116] [INFO] GTDB search result was written to GCA_023401435.1_ASM2340143v1_genomic.fna/result_gtdb.tsv
[2023-06-29 14:40:39,116] [INFO] ===== GTDB Search completed =====
[2023-06-29 14:40:39,119] [INFO] DFAST_QC result json was written to GCA_023401435.1_ASM2340143v1_genomic.fna/dqc_result.json
[2023-06-29 14:40:39,119] [INFO] DFAST_QC completed!
[2023-06-29 14:40:39,120] [INFO] Total running time: 0h0m51s