[2024-01-25 20:23:35,376] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:23:35,378] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:23:35,378] [INFO] DQC Reference Directory: /var/lib/cwl/stgf2bf7242-bea4-47d0-b7d7-54172fe85ad0/dqc_reference
[2024-01-25 20:23:36,532] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:23:36,533] [INFO] Task started: Prodigal
[2024-01-25 20:23:36,533] [INFO] Running command: gunzip -c /var/lib/cwl/stgd5b52ab1-2802-457c-9208-f6b05909d9fc/GCF_000620125.1_ASM62012v1_genomic.fna.gz | prodigal -d GCF_000620125.1_ASM62012v1_genomic.fna/cds.fna -a GCF_000620125.1_ASM62012v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:23:41,403] [INFO] Task succeeded: Prodigal
[2024-01-25 20:23:41,403] [INFO] Task started: HMMsearch
[2024-01-25 20:23:41,404] [INFO] Running command: hmmsearch --tblout GCF_000620125.1_ASM62012v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf2bf7242-bea4-47d0-b7d7-54172fe85ad0/dqc_reference/reference_markers.hmm GCF_000620125.1_ASM62012v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:23:41,617] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:23:41,618] [INFO] Found 6/6 markers.
[2024-01-25 20:23:41,645] [INFO] Query marker FASTA was written to GCF_000620125.1_ASM62012v1_genomic.fna/markers.fasta
[2024-01-25 20:23:41,646] [INFO] Task started: Blastn
[2024-01-25 20:23:41,646] [INFO] Running command: blastn -query GCF_000620125.1_ASM62012v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf2bf7242-bea4-47d0-b7d7-54172fe85ad0/dqc_reference/reference_markers.fasta -out GCF_000620125.1_ASM62012v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:23:42,177] [INFO] Task succeeded: Blastn
[2024-01-25 20:23:42,180] [INFO] Selected 22 target genomes.
[2024-01-25 20:23:42,180] [INFO] Target genome list was writen to GCF_000620125.1_ASM62012v1_genomic.fna/target_genomes.txt
[2024-01-25 20:23:42,218] [INFO] Task started: fastANI
[2024-01-25 20:23:42,218] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5b52ab1-2802-457c-9208-f6b05909d9fc/GCF_000620125.1_ASM62012v1_genomic.fna.gz --refList GCF_000620125.1_ASM62012v1_genomic.fna/target_genomes.txt --output GCF_000620125.1_ASM62012v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:23:53,754] [INFO] Task succeeded: fastANI
[2024-01-25 20:23:53,754] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf2bf7242-bea4-47d0-b7d7-54172fe85ad0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:23:53,754] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf2bf7242-bea4-47d0-b7d7-54172fe85ad0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:23:53,763] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:23:53,764] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:23:53,764] [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
Clostridiisalibacter paucivorans	strain=DSM 22131	GCA_000620125.1	408753	408753	type	True	100.0	1029	1036	95	conclusive
Anaeromonas gelatinilytica	strain=D2Q-14	GCA_016820635.1	2683194	2683194	type	True	76.7271	132	1036	95	below_threshold
Tissierella simiarum	strain=MSJ-40	GCA_018917865.1	2841534	2841534	type	True	76.4402	75	1036	95	below_threshold
Senegalia massiliensis	strain=SIT17	GCA_900626135.1	1720316	1720316	type	True	76.3071	119	1036	95	below_threshold
Anaeromonas frigoriresistens	strain=D2Q-11	GCA_016820655.1	2683708	2683708	type	True	76.1961	122	1036	95	below_threshold
Sporosalibacterium faouarense	strain=SOL3f37	GCA_016765695.1	516123	516123	type	True	75.9919	93	1036	95	below_threshold
Tissierella pigra	strain=WCA3-693-APC-4	GCA_009695605.1	2607614	2607614	type	True	75.9895	79	1036	95	below_threshold
Thermohalobacter berrensis	strain=CTT3	GCA_003609645.1	99594	99594	type	True	75.955	99	1036	95	below_threshold
Caldisalinibacter kiritimatiensis	strain=L21-TH-D2	GCA_000387765.1	1304284	1304284	type	True	75.8699	90	1036	95	below_threshold
Sporanaerobacter acetigenes	strain=DSM 13106	GCA_900130025.1	165813	165813	type	True	75.8498	67	1036	95	below_threshold
Caloranaerobacter ferrireducens	strain=DY22619	GCA_001730685.1	1323370	1323370	type	True	75.7875	73	1036	95	below_threshold
Romboutsia lituseburensis	strain=DSM 797	GCA_900103615.1	1537	1537	type	True	75.3887	66	1036	95	below_threshold
Romboutsia lituseburensis	strain=A25K	GCA_900002825.1	1537	1537	type	True	75.3886	65	1036	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:23:53,765] [INFO] DFAST Taxonomy check result was written to GCF_000620125.1_ASM62012v1_genomic.fna/tc_result.tsv
[2024-01-25 20:23:53,766] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:23:53,766] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:23:53,766] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf2bf7242-bea4-47d0-b7d7-54172fe85ad0/dqc_reference/checkm_data
[2024-01-25 20:23:53,767] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:23:53,803] [INFO] Task started: CheckM
[2024-01-25 20:23:53,803] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000620125.1_ASM62012v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000620125.1_ASM62012v1_genomic.fna/checkm_input GCF_000620125.1_ASM62012v1_genomic.fna/checkm_result
[2024-01-25 20:24:13,458] [INFO] Task succeeded: CheckM
[2024-01-25 20:24:13,459] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:24:13,475] [INFO] ===== Completeness check finished =====
[2024-01-25 20:24:13,475] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:24:13,476] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000620125.1_ASM62012v1_genomic.fna/markers.fasta)
[2024-01-25 20:24:13,476] [INFO] Task started: Blastn
[2024-01-25 20:24:13,476] [INFO] Running command: blastn -query GCF_000620125.1_ASM62012v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf2bf7242-bea4-47d0-b7d7-54172fe85ad0/dqc_reference/reference_markers_gtdb.fasta -out GCF_000620125.1_ASM62012v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:24:14,202] [INFO] Task succeeded: Blastn
[2024-01-25 20:24:14,205] [INFO] Selected 19 target genomes.
[2024-01-25 20:24:14,205] [INFO] Target genome list was writen to GCF_000620125.1_ASM62012v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:24:14,223] [INFO] Task started: fastANI
[2024-01-25 20:24:14,223] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5b52ab1-2802-457c-9208-f6b05909d9fc/GCF_000620125.1_ASM62012v1_genomic.fna.gz --refList GCF_000620125.1_ASM62012v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000620125.1_ASM62012v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:24:23,484] [INFO] Task succeeded: fastANI
[2024-01-25 20:24:23,494] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:24:23,494] [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_000620125.1	s__Clostridiisalibacter paucivorans	100.0	1029	1036	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Clostridiisalibacteraceae;g__Clostridiisalibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004103715.1	s__PP17-6a sp900095615	76.6476	54	1036	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__PP17-6a;g__PP17-6a	95.0	98.35	97.94	0.90	0.87	4	-
GCA_000751555.1	s__Anaerosalibacter massiliensis	76.3525	110	1036	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sporanaerobacteraceae;g__Anaerosalibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900626135.1	s__Senegalia massiliensis	76.3071	119	1036	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_900095305.1	s__Proteiniborus sp900095305	76.2444	52	1036	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_016820655.1	s__Senegalia sp016820655	76.1961	122	1036	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__SIT17;g__Senegalia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009711765.1	s__MES13 sp009711765	76.0351	149	1036	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__MES13;g__MES13	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016765695.1	s__Sporosalibacterium faouarense	75.9754	94	1036	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_009911265.1	s__Senegalia massiliensis_A	75.9441	123	1036	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__SIT17;g__Senegalia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002376545.1	s__Proteiniborus sp002376545	75.9098	64	1036	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Proteiniboraceae;g__Proteiniborus	95.0	99.93	99.93	0.97	0.97	2	-
GCA_012799055.1	s__JAAZMA01 sp012799055	75.8292	69	1036	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_009711785.1	s__MES13 sp009711785	75.7962	141	1036	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__MES13;g__MES13	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001730685.1	s__Caloranaerobacter ferrireducens	75.7875	73	1036	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_900103615.1	s__Romboutsia_D lituseburensis	75.3887	66	1036	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Romboutsia_D	95.0	99.98	99.98	1.00	1.00	2	-
GCF_900002575.1	s__Romboutsia_C hominis	74.9834	68	1036	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Romboutsia_C	95.0	98.29	95.25	0.93	0.90	6	-
--------------------------------------------------------------------------------
[2024-01-25 20:24:23,496] [INFO] GTDB search result was written to GCF_000620125.1_ASM62012v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:24:23,496] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:24:23,500] [INFO] DFAST_QC result json was written to GCF_000620125.1_ASM62012v1_genomic.fna/dqc_result.json
[2024-01-25 20:24:23,500] [INFO] DFAST_QC completed!
[2024-01-25 20:24:23,500] [INFO] Total running time: 0h0m48s