[2023-06-18 11:44:49,602] [INFO] DFAST_QC pipeline started.
[2023-06-18 11:44:49,606] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 11:44:49,607] [INFO] DQC Reference Directory: /var/lib/cwl/stg783a687c-e35f-4ff1-90be-2ee4b47df966/dqc_reference
[2023-06-18 11:44:50,858] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 11:44:50,859] [INFO] Task started: Prodigal
[2023-06-18 11:44:50,859] [INFO] Running command: gunzip -c /var/lib/cwl/stg2025de22-6790-4d01-ba2b-7168231a95ff/GCA_018713435.1_ASM1871343v1_genomic.fna.gz | prodigal -d GCA_018713435.1_ASM1871343v1_genomic.fna/cds.fna -a GCA_018713435.1_ASM1871343v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 11:44:55,827] [INFO] Task succeeded: Prodigal
[2023-06-18 11:44:55,827] [INFO] Task started: HMMsearch
[2023-06-18 11:44:55,827] [INFO] Running command: hmmsearch --tblout GCA_018713435.1_ASM1871343v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg783a687c-e35f-4ff1-90be-2ee4b47df966/dqc_reference/reference_markers.hmm GCA_018713435.1_ASM1871343v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 11:44:56,131] [INFO] Task succeeded: HMMsearch
[2023-06-18 11:44:56,132] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2025de22-6790-4d01-ba2b-7168231a95ff/GCA_018713435.1_ASM1871343v1_genomic.fna.gz]
[2023-06-18 11:44:56,177] [INFO] Query marker FASTA was written to GCA_018713435.1_ASM1871343v1_genomic.fna/markers.fasta
[2023-06-18 11:44:56,178] [INFO] Task started: Blastn
[2023-06-18 11:44:56,178] [INFO] Running command: blastn -query GCA_018713435.1_ASM1871343v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg783a687c-e35f-4ff1-90be-2ee4b47df966/dqc_reference/reference_markers.fasta -out GCA_018713435.1_ASM1871343v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 11:44:56,895] [INFO] Task succeeded: Blastn
[2023-06-18 11:44:56,899] [INFO] Selected 23 target genomes.
[2023-06-18 11:44:56,899] [INFO] Target genome list was writen to GCA_018713435.1_ASM1871343v1_genomic.fna/target_genomes.txt
[2023-06-18 11:44:56,900] [INFO] Task started: fastANI
[2023-06-18 11:44:56,900] [INFO] Running command: fastANI --query /var/lib/cwl/stg2025de22-6790-4d01-ba2b-7168231a95ff/GCA_018713435.1_ASM1871343v1_genomic.fna.gz --refList GCA_018713435.1_ASM1871343v1_genomic.fna/target_genomes.txt --output GCA_018713435.1_ASM1871343v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 11:45:10,087] [INFO] Task succeeded: fastANI
[2023-06-18 11:45:10,088] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg783a687c-e35f-4ff1-90be-2ee4b47df966/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 11:45:10,088] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg783a687c-e35f-4ff1-90be-2ee4b47df966/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 11:45:10,098] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 11:45:10,098] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 11:45:10,098] [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
Marvinbryantia formatexigens	strain=I-52	GCA_900102475.1	168384	168384	type	True	77.0324	77	653	95	below_threshold
Marvinbryantia formatexigens	strain=DSM 14469	GCA_025148285.1	168384	168384	type	True	76.9922	77	653	95	below_threshold
Massilistercora timonensis	strain=Marseille-P3756	GCA_900312975.1	2086584	2086584	type	True	76.8505	91	653	95	below_threshold
Wansuia hejianensis	strain=NSJ-29	GCA_014337215.1	2763667	2763667	type	True	76.6357	51	653	95	below_threshold
Diplocloster agilis	strain=ASD5720	GCA_019042275.1	2850323	2850323	type	True	76.6248	56	653	95	below_threshold
Schaedlerella arabinosiphila	strain=DSM 106076	GCA_003885045.1	2044587	2044587	type	True	76.5401	66	653	95	below_threshold
Enterocloster clostridioformis	strain=NCTC11224	GCA_900447015.1	1531	1531	suspected-type	True	76.1674	61	653	95	below_threshold
Enterocloster clostridioformis	strain=FDAARGOS_1529	GCA_020297485.1	1531	1531	suspected-type	True	76.1661	61	653	95	below_threshold
Murimonas intestini	strain=DSM 26524	GCA_024622195.1	1337051	1337051	type	True	75.8037	61	653	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 11:45:10,100] [INFO] DFAST Taxonomy check result was written to GCA_018713435.1_ASM1871343v1_genomic.fna/tc_result.tsv
[2023-06-18 11:45:10,101] [INFO] ===== Taxonomy check completed =====
[2023-06-18 11:45:10,101] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 11:45:10,102] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg783a687c-e35f-4ff1-90be-2ee4b47df966/dqc_reference/checkm_data
[2023-06-18 11:45:10,103] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 11:45:10,128] [INFO] Task started: CheckM
[2023-06-18 11:45:10,128] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018713435.1_ASM1871343v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018713435.1_ASM1871343v1_genomic.fna/checkm_input GCA_018713435.1_ASM1871343v1_genomic.fna/checkm_result
[2023-06-18 11:45:32,300] [INFO] Task succeeded: CheckM
[2023-06-18 11:45:32,302] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.41%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 11:45:32,328] [INFO] ===== Completeness check finished =====
[2023-06-18 11:45:32,329] [INFO] ===== Start GTDB Search =====
[2023-06-18 11:45:32,329] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018713435.1_ASM1871343v1_genomic.fna/markers.fasta)
[2023-06-18 11:45:32,329] [INFO] Task started: Blastn
[2023-06-18 11:45:32,330] [INFO] Running command: blastn -query GCA_018713435.1_ASM1871343v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg783a687c-e35f-4ff1-90be-2ee4b47df966/dqc_reference/reference_markers_gtdb.fasta -out GCA_018713435.1_ASM1871343v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 11:45:33,248] [INFO] Task succeeded: Blastn
[2023-06-18 11:45:33,253] [INFO] Selected 15 target genomes.
[2023-06-18 11:45:33,253] [INFO] Target genome list was writen to GCA_018713435.1_ASM1871343v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 11:45:33,260] [INFO] Task started: fastANI
[2023-06-18 11:45:33,260] [INFO] Running command: fastANI --query /var/lib/cwl/stg2025de22-6790-4d01-ba2b-7168231a95ff/GCA_018713435.1_ASM1871343v1_genomic.fna.gz --refList GCA_018713435.1_ASM1871343v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018713435.1_ASM1871343v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 11:45:40,450] [INFO] Task succeeded: fastANI
[2023-06-18 11:45:40,462] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 11:45:40,462] [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_018713435.1	s__Merdiplasma excrementigallinarum	100.0	652	653	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdiplasma	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900770325.1	s__Merdiplasma sp900770325	77.8798	151	653	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdiplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902778245.1	s__Merdiplasma sp902778245	77.7893	121	653	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdiplasma	95.0	98.95	98.95	0.63	0.63	2	-
GCA_902802515.1	s__Merdiplasma sp902802515	77.5795	135	653	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdiplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905207905.1	s__Merdiplasma sp905207905	77.5192	149	653	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdiplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902363135.1	s__Choladousia sp902363135	77.2163	63	653	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladousia	95.0	98.66	98.47	0.96	0.95	4	-
GCA_019116745.1	s__Lachnoclostridium_A stercorigallinarum	77.1601	70	653	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_A	95.0	99.47	99.47	0.89	0.89	2	-
GCA_018712785.1	s__Choladousia intestinavium	77.1314	111	653	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladousia	95.0	98.61	98.61	0.86	0.86	2	-
GCA_018712605.1	s__Choladousia intestinigallinarum	77.0932	102	653	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladousia	95.0	98.46	98.46	0.75	0.75	2	-
GCA_910586955.1	s__Merdisoma sp910586955	77.0048	63	653	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019118525.1	s__Bariatricus faecipullorum	76.6612	60	653	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902785635.1	s__Porcincola sp902785635	76.4099	58	653	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Porcincola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910575585.1	s__UBA3402 sp910575585	76.2974	66	653	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3402	95.0	99.89	99.85	0.96	0.96	3	-
GCA_900552095.1	s__Egerieimonas sp900552095	76.2213	52	653	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Egerieimonas	95.0	98.68	98.68	0.68	0.68	2	-
--------------------------------------------------------------------------------
[2023-06-18 11:45:40,464] [INFO] GTDB search result was written to GCA_018713435.1_ASM1871343v1_genomic.fna/result_gtdb.tsv
[2023-06-18 11:45:40,465] [INFO] ===== GTDB Search completed =====
[2023-06-18 11:45:40,468] [INFO] DFAST_QC result json was written to GCA_018713435.1_ASM1871343v1_genomic.fna/dqc_result.json
[2023-06-18 11:45:40,468] [INFO] DFAST_QC completed!
[2023-06-18 11:45:40,468] [INFO] Total running time: 0h0m51s