[2024-01-24 12:14:10,397] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:10,399] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:10,399] [INFO] DQC Reference Directory: /var/lib/cwl/stg18b9fd56-cb91-433c-839a-e0f5cbf657bf/dqc_reference
[2024-01-24 12:14:11,779] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:11,780] [INFO] Task started: Prodigal
[2024-01-24 12:14:11,780] [INFO] Running command: gunzip -c /var/lib/cwl/stged4cca81-3973-4378-814b-8b33d1404181/GCF_000621485.1_ASM62148v1_genomic.fna.gz | prodigal -d GCF_000621485.1_ASM62148v1_genomic.fna/cds.fna -a GCF_000621485.1_ASM62148v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:18,524] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:18,524] [INFO] Task started: HMMsearch
[2024-01-24 12:14:18,524] [INFO] Running command: hmmsearch --tblout GCF_000621485.1_ASM62148v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg18b9fd56-cb91-433c-839a-e0f5cbf657bf/dqc_reference/reference_markers.hmm GCF_000621485.1_ASM62148v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:18,839] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:18,840] [INFO] Found 6/6 markers.
[2024-01-24 12:14:18,876] [INFO] Query marker FASTA was written to GCF_000621485.1_ASM62148v1_genomic.fna/markers.fasta
[2024-01-24 12:14:18,876] [INFO] Task started: Blastn
[2024-01-24 12:14:18,876] [INFO] Running command: blastn -query GCF_000621485.1_ASM62148v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg18b9fd56-cb91-433c-839a-e0f5cbf657bf/dqc_reference/reference_markers.fasta -out GCF_000621485.1_ASM62148v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:19,583] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:19,587] [INFO] Selected 19 target genomes.
[2024-01-24 12:14:19,587] [INFO] Target genome list was writen to GCF_000621485.1_ASM62148v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:19,619] [INFO] Task started: fastANI
[2024-01-24 12:14:19,619] [INFO] Running command: fastANI --query /var/lib/cwl/stged4cca81-3973-4378-814b-8b33d1404181/GCF_000621485.1_ASM62148v1_genomic.fna.gz --refList GCF_000621485.1_ASM62148v1_genomic.fna/target_genomes.txt --output GCF_000621485.1_ASM62148v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:31,932] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:31,932] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg18b9fd56-cb91-433c-839a-e0f5cbf657bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:31,932] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg18b9fd56-cb91-433c-839a-e0f5cbf657bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:31,941] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:14:31,941] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:31,941] [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
Alkaliphilus transvaalensis	strain=ATCC 700919	GCA_000621485.1	114628	114628	type	True	100.0	1317	1319	95	conclusive
Alkaliphilus hydrothermalis	strain=DSM 25890	GCA_016908555.1	1482730	1482730	type	True	78.0601	243	1319	95	below_threshold
Alkaliphilus peptidifermentans	strain=DSM 18978	GCA_900101495.1	426129	426129	type	True	77.0793	156	1319	95	below_threshold
Anaerovirgula multivorans	strain=SCA	GCA_900188145.1	312168	312168	type	True	76.9721	132	1319	95	below_threshold
Alkaliphilus serpentinus	strain=LacT	GCA_009017255.1	1482731	1482731	type	True	76.9601	98	1319	95	below_threshold
Natronincola ferrireducens	strain=DSM 18346	GCA_900100845.1	393762	393762	type	True	76.5901	95	1319	95	below_threshold
Crassaminicella profunda	strain=Ra1766H	GCA_019884785.1	1286698	1286698	type	True	75.8631	60	1319	95	below_threshold
Paeniclostridium sordellii	strain=ATCC9714	GCA_000953675.1	1505	1505	type	True	75.5205	58	1319	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:31,943] [INFO] DFAST Taxonomy check result was written to GCF_000621485.1_ASM62148v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:31,943] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:31,943] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:31,943] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg18b9fd56-cb91-433c-839a-e0f5cbf657bf/dqc_reference/checkm_data
[2024-01-24 12:14:31,945] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:32,019] [INFO] Task started: CheckM
[2024-01-24 12:14:32,019] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000621485.1_ASM62148v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000621485.1_ASM62148v1_genomic.fna/checkm_input GCF_000621485.1_ASM62148v1_genomic.fna/checkm_result
[2024-01-24 12:14:59,533] [INFO] Task succeeded: CheckM
[2024-01-24 12:14:59,534] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:14:59,554] [INFO] ===== Completeness check finished =====
[2024-01-24 12:14:59,555] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:14:59,555] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000621485.1_ASM62148v1_genomic.fna/markers.fasta)
[2024-01-24 12:14:59,556] [INFO] Task started: Blastn
[2024-01-24 12:14:59,556] [INFO] Running command: blastn -query GCF_000621485.1_ASM62148v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg18b9fd56-cb91-433c-839a-e0f5cbf657bf/dqc_reference/reference_markers_gtdb.fasta -out GCF_000621485.1_ASM62148v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:00,643] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:00,646] [INFO] Selected 26 target genomes.
[2024-01-24 12:15:00,646] [INFO] Target genome list was writen to GCF_000621485.1_ASM62148v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:00,683] [INFO] Task started: fastANI
[2024-01-24 12:15:00,683] [INFO] Running command: fastANI --query /var/lib/cwl/stged4cca81-3973-4378-814b-8b33d1404181/GCF_000621485.1_ASM62148v1_genomic.fna.gz --refList GCF_000621485.1_ASM62148v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000621485.1_ASM62148v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:15,380] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:15,393] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:15,393] [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_000621485.1	s__Alkaliphilus transvaalensis	100.0	1317	1319	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Natronincolaceae;g__Alkaliphilus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016908555.1	s__Alkaliphilus hydrothermalis	78.0534	244	1319	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Natronincolaceae;g__Alkaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101495.1	s__Alkaliphilus_C peptidifermentans	77.0907	156	1319	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Natronincolaceae;g__Alkaliphilus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188145.1	s__Anaerovirgula multivorans	76.9721	132	1319	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Natronincolaceae;g__Anaerovirgula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009017255.1	s__LacT sp009017255	76.9601	98	1319	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Natronincolaceae;g__LacT	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100845.1	s__Natronincola ferrireducens	76.5572	94	1319	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Natronincolaceae;g__Natronincola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001854185.1	s__Clostridium_W formicaceticum	76.4545	115	1319	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Natronincolaceae;g__Clostridium_W	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900111615.1	s__Natronincola_A peptidivorans	76.2869	97	1319	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Natronincolaceae;g__Natronincola_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000953675.1	s__Paraclostridium sordellii	75.4899	58	1319	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Paraclostridium	95.0	98.12	96.78	0.93	0.89	59	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:15,395] [INFO] GTDB search result was written to GCF_000621485.1_ASM62148v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:15,395] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:15,398] [INFO] DFAST_QC result json was written to GCF_000621485.1_ASM62148v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:15,398] [INFO] DFAST_QC completed!
[2024-01-24 12:15:15,398] [INFO] Total running time: 0h1m5s