[2024-01-24 13:32:42,047] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:42,049] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:42,049] [INFO] DQC Reference Directory: /var/lib/cwl/stgd74b6328-349c-4bc5-8e42-26d168eed551/dqc_reference
[2024-01-24 13:32:43,373] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:43,374] [INFO] Task started: Prodigal
[2024-01-24 13:32:43,374] [INFO] Running command: gunzip -c /var/lib/cwl/stg3368d247-429b-4be0-a3c9-9e091c0a2e7d/GCF_000387765.1_L21-THTYG_genomic.fna.gz | prodigal -d GCF_000387765.1_L21-THTYG_genomic.fna/cds.fna -a GCF_000387765.1_L21-THTYG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:47,281] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:47,282] [INFO] Task started: HMMsearch
[2024-01-24 13:32:47,282] [INFO] Running command: hmmsearch --tblout GCF_000387765.1_L21-THTYG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd74b6328-349c-4bc5-8e42-26d168eed551/dqc_reference/reference_markers.hmm GCF_000387765.1_L21-THTYG_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:47,498] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:47,499] [INFO] Found 6/6 markers.
[2024-01-24 13:32:47,533] [INFO] Query marker FASTA was written to GCF_000387765.1_L21-THTYG_genomic.fna/markers.fasta
[2024-01-24 13:32:47,533] [INFO] Task started: Blastn
[2024-01-24 13:32:47,534] [INFO] Running command: blastn -query GCF_000387765.1_L21-THTYG_genomic.fna/markers.fasta -db /var/lib/cwl/stgd74b6328-349c-4bc5-8e42-26d168eed551/dqc_reference/reference_markers.fasta -out GCF_000387765.1_L21-THTYG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:48,146] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:48,150] [INFO] Selected 18 target genomes.
[2024-01-24 13:32:48,150] [INFO] Target genome list was writen to GCF_000387765.1_L21-THTYG_genomic.fna/target_genomes.txt
[2024-01-24 13:32:48,154] [INFO] Task started: fastANI
[2024-01-24 13:32:48,154] [INFO] Running command: fastANI --query /var/lib/cwl/stg3368d247-429b-4be0-a3c9-9e091c0a2e7d/GCF_000387765.1_L21-THTYG_genomic.fna.gz --refList GCF_000387765.1_L21-THTYG_genomic.fna/target_genomes.txt --output GCF_000387765.1_L21-THTYG_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:56,711] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:56,712] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd74b6328-349c-4bc5-8e42-26d168eed551/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:56,712] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd74b6328-349c-4bc5-8e42-26d168eed551/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:56,722] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:56,722] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:56,723] [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
Caldisalinibacter kiritimatiensis	strain=L21-TH-D2	GCA_000387765.1	1304284	1304284	type	True	100.0	797	806	95	conclusive
Thermohalobacter berrensis	strain=CTT3	GCA_003609645.1	99594	99594	type	True	77.2451	173	806	95	below_threshold
Caloranaerobacter ferrireducens	strain=DY22619	GCA_001730685.1	1323370	1323370	type	True	76.6669	148	806	95	below_threshold
Sporosalibacterium faouarense	strain=SOL3f37	GCA_016765695.1	516123	516123	type	True	76.396	112	806	95	below_threshold
Anaeromonas gelatinilytica	strain=D2Q-14	GCA_016820635.1	2683194	2683194	type	True	76.3716	100	806	95	below_threshold
Senegalia massiliensis	strain=SIT17	GCA_900626135.1	1720316	1720316	type	True	76.177	102	806	95	below_threshold
Gottschalkia purinilytica	strain=DSM 1384	GCA_001190785.1	1503	1503	type	True	75.9818	102	806	95	below_threshold
Romboutsia timonensis	strain=Marseille-P326	GCA_900106845.1	1776391	1776391	type	True	75.7496	56	806	95	below_threshold
Tissierella simiarum	strain=MSJ-40	GCA_018917865.1	2841534	2841534	type	True	75.557	75	806	95	below_threshold
Tissierella pigra	strain=WCA3-693-APC-4	GCA_009695605.1	2607614	2607614	type	True	75.4406	69	806	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:56,725] [INFO] DFAST Taxonomy check result was written to GCF_000387765.1_L21-THTYG_genomic.fna/tc_result.tsv
[2024-01-24 13:32:56,726] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:56,726] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:56,726] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd74b6328-349c-4bc5-8e42-26d168eed551/dqc_reference/checkm_data
[2024-01-24 13:32:56,728] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:56,757] [INFO] Task started: CheckM
[2024-01-24 13:32:56,758] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000387765.1_L21-THTYG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000387765.1_L21-THTYG_genomic.fna/checkm_input GCF_000387765.1_L21-THTYG_genomic.fna/checkm_result
[2024-01-24 13:33:16,892] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:16,893] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:16,909] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:16,910] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:16,910] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000387765.1_L21-THTYG_genomic.fna/markers.fasta)
[2024-01-24 13:33:16,910] [INFO] Task started: Blastn
[2024-01-24 13:33:16,910] [INFO] Running command: blastn -query GCF_000387765.1_L21-THTYG_genomic.fna/markers.fasta -db /var/lib/cwl/stgd74b6328-349c-4bc5-8e42-26d168eed551/dqc_reference/reference_markers_gtdb.fasta -out GCF_000387765.1_L21-THTYG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:17,710] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:17,713] [INFO] Selected 22 target genomes.
[2024-01-24 13:33:17,713] [INFO] Target genome list was writen to GCF_000387765.1_L21-THTYG_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:17,738] [INFO] Task started: fastANI
[2024-01-24 13:33:17,738] [INFO] Running command: fastANI --query /var/lib/cwl/stg3368d247-429b-4be0-a3c9-9e091c0a2e7d/GCF_000387765.1_L21-THTYG_genomic.fna.gz --refList GCF_000387765.1_L21-THTYG_genomic.fna/target_genomes_gtdb.txt --output GCF_000387765.1_L21-THTYG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:26,666] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:26,676] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:26,676] [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_000387765.1	s__Caldisalinibacter kiritimatiensis	100.0	797	806	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Caldisalinibacteraceae;g__Caldisalinibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003609645.1	s__Thermohalobacter berrensis	77.2133	175	806	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Thermohalobacteraceae;g__Thermohalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001316435.1	s__Caloranaerobacter sp001316435	76.9818	120	806	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Thermohalobacteraceae;g__Caloranaerobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001730685.1	s__Caloranaerobacter ferrireducens	76.6377	150	806	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Thermohalobacteraceae;g__Caloranaerobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016765695.1	s__Sporosalibacterium faouarense	76.3951	112	806	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__VENL01;g__Sporosalibacterium	95.0	99.35	99.35	0.89	0.89	2	-
GCF_016820635.1	s__Senegalia sp016820635	76.3906	99	806	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_001190785.1	s__Gottschalkia_A purinilytica	75.9965	101	806	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Gottschalkiaceae;g__Gottschalkia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009696605.1	s__Anaerosalibacter bizertensis	75.7755	79	806	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sporanaerobacteraceae;g__Anaerosalibacter	95.0	98.53	98.48	0.86	0.84	3	-
GCF_900095305.1	s__Proteiniborus sp900095305	75.6629	67	806	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Proteiniboraceae;g__Proteiniborus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018917865.1	s__MSJ-40 sp018917865	75.557	75	806	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	-
GCF_009695605.1	s__DSM105185 sp009695605	75.4406	69	806	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tissierellaceae;g__DSM105185	95.0	99.10	99.10	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:26,678] [INFO] GTDB search result was written to GCF_000387765.1_L21-THTYG_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:26,679] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:26,681] [INFO] DFAST_QC result json was written to GCF_000387765.1_L21-THTYG_genomic.fna/dqc_result.json
[2024-01-24 13:33:26,682] [INFO] DFAST_QC completed!
[2024-01-24 13:33:26,682] [INFO] Total running time: 0h0m45s