[2024-01-24 14:30:59,643] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:59,644] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:59,645] [INFO] DQC Reference Directory: /var/lib/cwl/stg6b895b13-dcf5-4e13-90d0-87aa4c4f5bec/dqc_reference
[2024-01-24 14:31:01,052] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:01,053] [INFO] Task started: Prodigal
[2024-01-24 14:31:01,053] [INFO] Running command: gunzip -c /var/lib/cwl/stgc62ddced-d715-403f-ba41-1ca01851da14/GCF_014701195.1_ASM1470119v1_genomic.fna.gz | prodigal -d GCF_014701195.1_ASM1470119v1_genomic.fna/cds.fna -a GCF_014701195.1_ASM1470119v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:05,578] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:05,578] [INFO] Task started: HMMsearch
[2024-01-24 14:31:05,578] [INFO] Running command: hmmsearch --tblout GCF_014701195.1_ASM1470119v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6b895b13-dcf5-4e13-90d0-87aa4c4f5bec/dqc_reference/reference_markers.hmm GCF_014701195.1_ASM1470119v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:05,876] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:05,878] [INFO] Found 6/6 markers.
[2024-01-24 14:31:05,907] [INFO] Query marker FASTA was written to GCF_014701195.1_ASM1470119v1_genomic.fna/markers.fasta
[2024-01-24 14:31:05,907] [INFO] Task started: Blastn
[2024-01-24 14:31:05,907] [INFO] Running command: blastn -query GCF_014701195.1_ASM1470119v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b895b13-dcf5-4e13-90d0-87aa4c4f5bec/dqc_reference/reference_markers.fasta -out GCF_014701195.1_ASM1470119v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:06,539] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:06,542] [INFO] Selected 15 target genomes.
[2024-01-24 14:31:06,543] [INFO] Target genome list was writen to GCF_014701195.1_ASM1470119v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:06,549] [INFO] Task started: fastANI
[2024-01-24 14:31:06,549] [INFO] Running command: fastANI --query /var/lib/cwl/stgc62ddced-d715-403f-ba41-1ca01851da14/GCF_014701195.1_ASM1470119v1_genomic.fna.gz --refList GCF_014701195.1_ASM1470119v1_genomic.fna/target_genomes.txt --output GCF_014701195.1_ASM1470119v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:14,069] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:14,069] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6b895b13-dcf5-4e13-90d0-87aa4c4f5bec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:14,070] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6b895b13-dcf5-4e13-90d0-87aa4c4f5bec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:14,080] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:31:14,081] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:14,081] [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
Tepiditoga spiralis	strain=sy52	GCA_014701195.1	2108365	2108365	type	True	100.0	833	834	95	conclusive
Marinitoga litoralis	strain=DSM 21709	GCA_016908145.1	570855	570855	type	True	75.7678	176	834	95	below_threshold
Marinitoga hydrogenitolerans	strain=DSM 16785	GCA_900129175.1	287990	287990	type	True	75.6	154	834	95	below_threshold
Romboutsia hominis	strain=FRIFI	GCA_900002575.1	1507512	1507512	type	True	74.9839	92	834	95	below_threshold
Clostridium fallax	strain=NCTC8380	GCA_900461065.1	1533	1533	type	True	74.9593	105	834	95	below_threshold
Clostridium massiliodielmoense	strain=MT26	GCA_900176615.1	1776385	1776385	type	True	74.9537	81	834	95	below_threshold
Clostridium cochlearium	strain=NCTC13027	GCA_900187165.1	1494	1494	type	True	74.9196	83	834	95	below_threshold
Arcobacter suis	strain=CECT7833	GCA_004023465.1	1278212	1278212	type	True	74.7769	71	834	95	below_threshold
Cetobacterium ceti	strain=ATCC 700028	GCA_900167275.1	180163	180163	type	True	74.7217	100	834	95	below_threshold
Terrisporobacter mayombei	strain=DSM 6539	GCA_020748465.1	1541	1541	type	True	74.6423	91	834	95	below_threshold
Clostridium fallax	strain=DSM 2631	GCA_900129365.1	1533	1533	type	True	74.6215	97	834	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:14,088] [INFO] DFAST Taxonomy check result was written to GCF_014701195.1_ASM1470119v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:14,089] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:14,089] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:14,090] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6b895b13-dcf5-4e13-90d0-87aa4c4f5bec/dqc_reference/checkm_data
[2024-01-24 14:31:14,091] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:14,128] [INFO] Task started: CheckM
[2024-01-24 14:31:14,129] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014701195.1_ASM1470119v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014701195.1_ASM1470119v1_genomic.fna/checkm_input GCF_014701195.1_ASM1470119v1_genomic.fna/checkm_result
[2024-01-24 14:31:35,236] [INFO] Task succeeded: CheckM
[2024-01-24 14:31:35,238] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.93%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:31:35,262] [INFO] ===== Completeness check finished =====
[2024-01-24 14:31:35,263] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:31:35,263] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014701195.1_ASM1470119v1_genomic.fna/markers.fasta)
[2024-01-24 14:31:35,264] [INFO] Task started: Blastn
[2024-01-24 14:31:35,264] [INFO] Running command: blastn -query GCF_014701195.1_ASM1470119v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b895b13-dcf5-4e13-90d0-87aa4c4f5bec/dqc_reference/reference_markers_gtdb.fasta -out GCF_014701195.1_ASM1470119v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:36,154] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:36,159] [INFO] Selected 18 target genomes.
[2024-01-24 14:31:36,159] [INFO] Target genome list was writen to GCF_014701195.1_ASM1470119v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:31:36,173] [INFO] Task started: fastANI
[2024-01-24 14:31:36,174] [INFO] Running command: fastANI --query /var/lib/cwl/stgc62ddced-d715-403f-ba41-1ca01851da14/GCF_014701195.1_ASM1470119v1_genomic.fna.gz --refList GCF_014701195.1_ASM1470119v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014701195.1_ASM1470119v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:31:43,335] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:43,343] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:31:43,344] [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_014701195.1	s__Tepiditoga spiralis	100.0	833	834	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Petrotogales;f__Petrotogaceae;g__Tepiditoga	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003148465.1	s__Oceanotoga teriensis	76.062	248	834	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Petrotogales;f__Petrotogaceae;g__Oceanotoga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908145.1	s__Marinitoga litoralis	75.79	170	834	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Petrotogales;f__Petrotogaceae;g__Marinitoga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129175.1	s__Marinitoga hydrogenitolerans	75.6216	151	834	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Petrotogales;f__Petrotogaceae;g__Marinitoga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187165.1	s__Clostridium_G cochlearium	74.9214	81	834	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_G	95.0	99.06	98.56	0.90	0.85	10	-
GCF_009268105.1	s__Phytoplasma sacchari	74.9205	73	834	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__Phytoplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016744535.1	s__BB28 sp016744535	74.7008	79	834	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__BB28;g__BB28	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129365.1	s__Clostridium_AH fallax	74.6206	94	834	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AH	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:31:43,351] [INFO] GTDB search result was written to GCF_014701195.1_ASM1470119v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:31:43,352] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:31:43,359] [INFO] DFAST_QC result json was written to GCF_014701195.1_ASM1470119v1_genomic.fna/dqc_result.json
[2024-01-24 14:31:43,359] [INFO] DFAST_QC completed!
[2024-01-24 14:31:43,359] [INFO] Total running time: 0h0m44s