[2024-01-24 13:48:43,144] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:43,146] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:43,147] [INFO] DQC Reference Directory: /var/lib/cwl/stg6049ae6d-09b4-4d5c-9d3f-0f12c65e37c2/dqc_reference
[2024-01-24 13:48:44,425] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:48:44,426] [INFO] Task started: Prodigal
[2024-01-24 13:48:44,426] [INFO] Running command: gunzip -c /var/lib/cwl/stgb4a4b0df-9953-4908-a724-00ad55b45a36/GCF_018917865.1_ASM1891786v1_genomic.fna.gz | prodigal -d GCF_018917865.1_ASM1891786v1_genomic.fna/cds.fna -a GCF_018917865.1_ASM1891786v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:48:50,802] [INFO] Task succeeded: Prodigal
[2024-01-24 13:48:50,802] [INFO] Task started: HMMsearch
[2024-01-24 13:48:50,802] [INFO] Running command: hmmsearch --tblout GCF_018917865.1_ASM1891786v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6049ae6d-09b4-4d5c-9d3f-0f12c65e37c2/dqc_reference/reference_markers.hmm GCF_018917865.1_ASM1891786v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:48:51,080] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:48:51,081] [INFO] Found 6/6 markers.
[2024-01-24 13:48:51,118] [INFO] Query marker FASTA was written to GCF_018917865.1_ASM1891786v1_genomic.fna/markers.fasta
[2024-01-24 13:48:51,119] [INFO] Task started: Blastn
[2024-01-24 13:48:51,119] [INFO] Running command: blastn -query GCF_018917865.1_ASM1891786v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6049ae6d-09b4-4d5c-9d3f-0f12c65e37c2/dqc_reference/reference_markers.fasta -out GCF_018917865.1_ASM1891786v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:48:51,701] [INFO] Task succeeded: Blastn
[2024-01-24 13:48:51,705] [INFO] Selected 14 target genomes.
[2024-01-24 13:48:51,706] [INFO] Target genome list was writen to GCF_018917865.1_ASM1891786v1_genomic.fna/target_genomes.txt
[2024-01-24 13:48:51,712] [INFO] Task started: fastANI
[2024-01-24 13:48:51,712] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4a4b0df-9953-4908-a724-00ad55b45a36/GCF_018917865.1_ASM1891786v1_genomic.fna.gz --refList GCF_018917865.1_ASM1891786v1_genomic.fna/target_genomes.txt --output GCF_018917865.1_ASM1891786v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:48:59,690] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:59,691] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6049ae6d-09b4-4d5c-9d3f-0f12c65e37c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:48:59,692] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6049ae6d-09b4-4d5c-9d3f-0f12c65e37c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:48:59,709] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:48:59,710] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:48:59,710] [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
Tissierella simiarum	strain=MSJ-40	GCA_018917865.1	2841534	2841534	type	True	100.0	1335	1336	95	conclusive
Tissierella pigra	strain=WCA3-693-APC-4	GCA_009695605.1	2607614	2607614	type	True	78.8216	326	1336	95	below_threshold
Tissierella praeacuta	strain=NCTC11158	GCA_900460335.1	43131	43131	type	True	78.6653	326	1336	95	below_threshold
Tissierella praeacuta	strain=DSM 18095	GCA_900128955.1	43131	43131	type	True	78.5677	313	1336	95	below_threshold
Keratinibaculum paraultunense	strain=KD-1	GCA_016767175.1	1278232	1278232	type	True	76.9345	176	1336	95	below_threshold
Sporanaerobacter acetigenes	strain=DSM 13106	GCA_900130025.1	165813	165813	type	True	76.8041	200	1336	95	below_threshold
Keratinibaculum paraultunense	strain=DSM 26752	GCA_004343355.1	1278232	1278232	type	True	76.7468	176	1336	95	below_threshold
Tissierella creatinophila	strain=DSM 6911	GCA_001940565.1	79681	79681	type	True	76.4633	123	1336	95	below_threshold
Senegalia massiliensis	strain=SIT17	GCA_900626135.1	1720316	1720316	type	True	76.042	120	1336	95	below_threshold
Sporosalibacterium faouarense	strain=SOL3f37	GCA_016765695.1	516123	516123	type	True	75.5662	78	1336	95	below_threshold
Crassaminicella profunda	strain=Ra1766H	GCA_019884785.1	1286698	1286698	type	True	75.5314	100	1336	95	below_threshold
Caldisalinibacter kiritimatiensis	strain=L21-TH-D2	GCA_000387765.1	1304284	1304284	type	True	75.5253	79	1336	95	below_threshold
Clostridium saccharobutylicum	strain=DSM 13864	GCA_000473995.1	169679	169679	type	True	75.4964	76	1336	95	below_threshold
Tepidibacter formicigenes	strain=DSM 15518	GCA_900142235.1	227138	227138	type	True	75.4635	101	1336	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:48:59,711] [INFO] DFAST Taxonomy check result was written to GCF_018917865.1_ASM1891786v1_genomic.fna/tc_result.tsv
[2024-01-24 13:48:59,712] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:48:59,712] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:48:59,712] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6049ae6d-09b4-4d5c-9d3f-0f12c65e37c2/dqc_reference/checkm_data
[2024-01-24 13:48:59,714] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:48:59,756] [INFO] Task started: CheckM
[2024-01-24 13:48:59,756] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018917865.1_ASM1891786v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018917865.1_ASM1891786v1_genomic.fna/checkm_input GCF_018917865.1_ASM1891786v1_genomic.fna/checkm_result
[2024-01-24 13:49:25,383] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:25,384] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:25,408] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:25,409] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:25,409] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018917865.1_ASM1891786v1_genomic.fna/markers.fasta)
[2024-01-24 13:49:25,410] [INFO] Task started: Blastn
[2024-01-24 13:49:25,410] [INFO] Running command: blastn -query GCF_018917865.1_ASM1891786v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6049ae6d-09b4-4d5c-9d3f-0f12c65e37c2/dqc_reference/reference_markers_gtdb.fasta -out GCF_018917865.1_ASM1891786v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:26,231] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:26,239] [INFO] Selected 17 target genomes.
[2024-01-24 13:49:26,240] [INFO] Target genome list was writen to GCF_018917865.1_ASM1891786v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:26,253] [INFO] Task started: fastANI
[2024-01-24 13:49:26,253] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4a4b0df-9953-4908-a724-00ad55b45a36/GCF_018917865.1_ASM1891786v1_genomic.fna.gz --refList GCF_018917865.1_ASM1891786v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018917865.1_ASM1891786v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:49:34,876] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:34,889] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:49:34,889] [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_018917865.1	s__MSJ-40 sp018917865	100.0	1335	1336	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tissierellaceae;g__MSJ-40	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002266425.1	s__Tissierella carlieri	78.9193	372	1336	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tissierellaceae;g__Tissierella	95.0	97.51	96.78	0.86	0.84	3	-
GCF_009695605.1	s__DSM105185 sp009695605	78.834	325	1336	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tissierellaceae;g__DSM105185	95.0	99.10	99.10	0.90	0.90	2	-
GCF_900128955.1	s__Tissierella praeacuta	78.5948	311	1336	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tissierellaceae;g__Tissierella	95.0	99.01	98.20	0.93	0.86	5	-
GCA_001282665.1	s__Mt11 sp001282665	78.1233	295	1336	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tepidimicrobiaceae;g__Mt11	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002398845.1	s__Mt11 sp002398845	77.1195	128	1336	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tepidimicrobiaceae;g__Mt11	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900155565.1	s__Anaerosalibacter_A sp900155565	76.9557	163	1336	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sporanaerobacteraceae;g__Anaerosalibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016767175.1	s__Keratinibaculum paraultunense	76.9361	175	1336	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tepidimicrobiaceae;g__Keratinibaculum	95.0	100.00	100.00	1.00	1.00	2	-
GCA_014385225.1	s__JACRTK01 sp014385225	76.8767	157	1336	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tissierellaceae;g__JACRTK01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000511955.1	s__Schnuerera ultunensis	76.776	179	1336	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tepidimicrobiaceae;g__Schnuerera	95.0	99.51	99.51	0.99	0.99	2	-
GCA_012799055.1	s__JAAZMA01 sp012799055	76.6776	143	1336	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tepidimicrobiaceae;g__JAAZMA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012798935.1	s__JAAZMG01 sp012798935	76.6435	121	1336	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tepidimicrobiaceae;g__JAAZMG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012728075.1	s__Keratinibaculum sp012728075	76.6088	148	1336	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tepidimicrobiaceae;g__Keratinibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012728125.1	s__JAAYFT01 sp012728125	76.3946	105	1336	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tissierellaceae;g__JAAYFT01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009911265.1	s__Senegalia massiliensis_A	76.0438	114	1336	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__SIT17;g__Senegalia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900626135.1	s__Senegalia massiliensis	76.0204	118	1336	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__SIT17;g__Senegalia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016765695.1	s__Sporosalibacterium faouarense	75.5662	78	1336	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__VENL01;g__Sporosalibacterium	95.0	99.35	99.35	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:49:34,891] [INFO] GTDB search result was written to GCF_018917865.1_ASM1891786v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:49:34,892] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:49:34,898] [INFO] DFAST_QC result json was written to GCF_018917865.1_ASM1891786v1_genomic.fna/dqc_result.json
[2024-01-24 13:49:34,898] [INFO] DFAST_QC completed!
[2024-01-24 13:49:34,899] [INFO] Total running time: 0h0m52s