[2024-01-24 13:48:43,330] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:43,331] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:43,332] [INFO] DQC Reference Directory: /var/lib/cwl/stg2d74ce43-f4b2-458a-8eef-1aed70064c93/dqc_reference
[2024-01-24 13:48:44,554] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:48:44,555] [INFO] Task started: Prodigal
[2024-01-24 13:48:44,555] [INFO] Running command: gunzip -c /var/lib/cwl/stg4593636e-03ab-492a-8ca0-e1f132996467/GCF_004116555.1_ASM411655v1_genomic.fna.gz | prodigal -d GCF_004116555.1_ASM411655v1_genomic.fna/cds.fna -a GCF_004116555.1_ASM411655v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:48:48,557] [INFO] Task succeeded: Prodigal
[2024-01-24 13:48:48,558] [INFO] Task started: HMMsearch
[2024-01-24 13:48:48,558] [INFO] Running command: hmmsearch --tblout GCF_004116555.1_ASM411655v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2d74ce43-f4b2-458a-8eef-1aed70064c93/dqc_reference/reference_markers.hmm GCF_004116555.1_ASM411655v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:48:48,803] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:48:48,805] [INFO] Found 6/6 markers.
[2024-01-24 13:48:48,833] [INFO] Query marker FASTA was written to GCF_004116555.1_ASM411655v1_genomic.fna/markers.fasta
[2024-01-24 13:48:48,833] [INFO] Task started: Blastn
[2024-01-24 13:48:48,833] [INFO] Running command: blastn -query GCF_004116555.1_ASM411655v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d74ce43-f4b2-458a-8eef-1aed70064c93/dqc_reference/reference_markers.fasta -out GCF_004116555.1_ASM411655v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:48:49,408] [INFO] Task succeeded: Blastn
[2024-01-24 13:48:49,412] [INFO] Selected 9 target genomes.
[2024-01-24 13:48:49,413] [INFO] Target genome list was writen to GCF_004116555.1_ASM411655v1_genomic.fna/target_genomes.txt
[2024-01-24 13:48:49,424] [INFO] Task started: fastANI
[2024-01-24 13:48:49,424] [INFO] Running command: fastANI --query /var/lib/cwl/stg4593636e-03ab-492a-8ca0-e1f132996467/GCF_004116555.1_ASM411655v1_genomic.fna.gz --refList GCF_004116555.1_ASM411655v1_genomic.fna/target_genomes.txt --output GCF_004116555.1_ASM411655v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:48:55,397] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:55,398] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2d74ce43-f4b2-458a-8eef-1aed70064c93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:48:55,398] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2d74ce43-f4b2-458a-8eef-1aed70064c93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:48:55,406] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:48:55,407] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:48:55,407] [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
Malaciobacter mytili	strain=CECT 7386	GCA_004116555.1	603050	603050	type	True	100.0	934	940	95	conclusive
Malaciobacter mytili	strain=LMG 24559	GCA_003346775.1	603050	603050	type	True	99.9985	939	940	95	conclusive
Malaciobacter halophilus	strain=DSM 18005	GCA_002837275.1	197482	197482	type	True	82.5548	613	940	95	below_threshold
Malaciobacter canalis	strain=LMG 29148	GCA_008000835.1	1912871	1912871	type	True	82.3605	613	940	95	below_threshold
Malaciobacter canalis	strain=F138-33	GCA_002723485.1	1912871	1912871	type	True	82.291	609	940	95	below_threshold
Malaciobacter marinus	strain=JCM 15502	GCA_003544855.1	505249	505249	type	True	82.1428	613	940	95	below_threshold
Malaciobacter molluscorum	strain=F98-3	GCA_002701265.1	1032072	1032072	type	True	81.7636	564	940	95	below_threshold
Malaciobacter molluscorum	strain=CECT 7696	GCA_003544935.1	1032072	1032072	type	True	81.7392	584	940	95	below_threshold
Arcobacter ellisii	strain=LMG 26155	GCA_003544915.1	913109	913109	type	True	79.7544	457	940	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:48:55,408] [INFO] DFAST Taxonomy check result was written to GCF_004116555.1_ASM411655v1_genomic.fna/tc_result.tsv
[2024-01-24 13:48:55,409] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:48:55,409] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:48:55,409] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2d74ce43-f4b2-458a-8eef-1aed70064c93/dqc_reference/checkm_data
[2024-01-24 13:48:55,410] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:48:55,440] [INFO] Task started: CheckM
[2024-01-24 13:48:55,440] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004116555.1_ASM411655v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004116555.1_ASM411655v1_genomic.fna/checkm_input GCF_004116555.1_ASM411655v1_genomic.fna/checkm_result
[2024-01-24 13:49:14,988] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:14,990] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:15,009] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:15,009] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:15,010] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004116555.1_ASM411655v1_genomic.fna/markers.fasta)
[2024-01-24 13:49:15,010] [INFO] Task started: Blastn
[2024-01-24 13:49:15,010] [INFO] Running command: blastn -query GCF_004116555.1_ASM411655v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d74ce43-f4b2-458a-8eef-1aed70064c93/dqc_reference/reference_markers_gtdb.fasta -out GCF_004116555.1_ASM411655v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:15,742] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:15,745] [INFO] Selected 8 target genomes.
[2024-01-24 13:49:15,745] [INFO] Target genome list was writen to GCF_004116555.1_ASM411655v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:15,751] [INFO] Task started: fastANI
[2024-01-24 13:49:15,751] [INFO] Running command: fastANI --query /var/lib/cwl/stg4593636e-03ab-492a-8ca0-e1f132996467/GCF_004116555.1_ASM411655v1_genomic.fna.gz --refList GCF_004116555.1_ASM411655v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004116555.1_ASM411655v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:49:20,873] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:20,881] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:49:20,881] [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_003346775.1	s__Malaciobacter mytili	99.9985	939	940	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Malaciobacter	95.0	99.45	98.91	0.96	0.92	3	conclusive
GCF_002837275.1	s__Malaciobacter halophilus	82.5678	612	940	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Malaciobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003544855.1	s__Malaciobacter marinus	82.1806	610	940	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Malaciobacter	95.0	98.03	95.41	0.91	0.86	14	-
GCA_004116725.1	s__Malaciobacter sp004116725	82.0761	570	940	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Malaciobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003544935.1	s__Malaciobacter molluscorum	81.7142	586	940	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Malaciobacter	95.0	99.44	98.88	0.96	0.91	3	-
GCA_004116495.1	s__Malaciobacter sp004116495	81.6311	562	940	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Malaciobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003544915.1	s__Aliarcobacter ellisii	79.7881	454	940	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.73	97.46	0.92	0.84	3	-
GCF_004214815.1	s__Aliarcobacter thereius	78.6497	299	940	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.14	98.62	0.93	0.89	8	-
--------------------------------------------------------------------------------
[2024-01-24 13:49:20,883] [INFO] GTDB search result was written to GCF_004116555.1_ASM411655v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:49:20,883] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:49:20,887] [INFO] DFAST_QC result json was written to GCF_004116555.1_ASM411655v1_genomic.fna/dqc_result.json
[2024-01-24 13:49:20,888] [INFO] DFAST_QC completed!
[2024-01-24 13:49:20,888] [INFO] Total running time: 0h0m38s