[2024-01-24 12:36:24,217] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:24,218] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:24,219] [INFO] DQC Reference Directory: /var/lib/cwl/stg99f5f884-32fb-4627-ac5a-d75d6d035310/dqc_reference
[2024-01-24 12:36:25,600] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:25,601] [INFO] Task started: Prodigal
[2024-01-24 12:36:25,601] [INFO] Running command: gunzip -c /var/lib/cwl/stg1b11c60f-0fe2-401b-b815-1a28d153bb64/GCF_004217115.1_ASM421711v1_genomic.fna.gz | prodigal -d GCF_004217115.1_ASM421711v1_genomic.fna/cds.fna -a GCF_004217115.1_ASM421711v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:36:41,628] [INFO] Task succeeded: Prodigal
[2024-01-24 12:36:41,628] [INFO] Task started: HMMsearch
[2024-01-24 12:36:41,628] [INFO] Running command: hmmsearch --tblout GCF_004217115.1_ASM421711v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg99f5f884-32fb-4627-ac5a-d75d6d035310/dqc_reference/reference_markers.hmm GCF_004217115.1_ASM421711v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:36:41,923] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:36:41,925] [INFO] Found 6/6 markers.
[2024-01-24 12:36:41,961] [INFO] Query marker FASTA was written to GCF_004217115.1_ASM421711v1_genomic.fna/markers.fasta
[2024-01-24 12:36:41,961] [INFO] Task started: Blastn
[2024-01-24 12:36:41,961] [INFO] Running command: blastn -query GCF_004217115.1_ASM421711v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg99f5f884-32fb-4627-ac5a-d75d6d035310/dqc_reference/reference_markers.fasta -out GCF_004217115.1_ASM421711v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:36:42,553] [INFO] Task succeeded: Blastn
[2024-01-24 12:36:42,556] [INFO] Selected 13 target genomes.
[2024-01-24 12:36:42,557] [INFO] Target genome list was writen to GCF_004217115.1_ASM421711v1_genomic.fna/target_genomes.txt
[2024-01-24 12:36:42,562] [INFO] Task started: fastANI
[2024-01-24 12:36:42,563] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b11c60f-0fe2-401b-b815-1a28d153bb64/GCF_004217115.1_ASM421711v1_genomic.fna.gz --refList GCF_004217115.1_ASM421711v1_genomic.fna/target_genomes.txt --output GCF_004217115.1_ASM421711v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:36:53,851] [INFO] Task succeeded: fastANI
[2024-01-24 12:36:53,851] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg99f5f884-32fb-4627-ac5a-d75d6d035310/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:36:53,851] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg99f5f884-32fb-4627-ac5a-d75d6d035310/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:36:53,860] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:36:53,860] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:36:53,860] [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
Ancylomarina subtilis	strain=DSM 28825	GCA_004217115.1	1639035	1639035	type	True	100.0	1327	1327	95	conclusive
Ancylomarina salipaludis	strain=SHSM-M15	GCA_004122035.1	2501299	2501299	type	True	88.4282	1112	1327	95	below_threshold
Marinifilum breve	strain=JC075	GCA_003202155.1	2184082	2184082	type	True	78.1372	240	1327	95	below_threshold
Marinifilum flexuosum	strain=DSM 21950	GCA_003610555.1	1117708	1117708	type	True	77.9517	246	1327	95	below_threshold
Marinifilum fragile	strain=JCM 15579	GCA_001310955.1	570161	570161	type	True	77.9053	244	1327	95	below_threshold
Labilibaculum manganireducens	strain=59.10-2M	GCA_002843385.1	1940525	1940525	type	True	77.7972	220	1327	95	below_threshold
Ancylomarina longa	strain=T3-2 S1-C	GCA_003996985.1	2487017	2487017	type	True	77.5597	166	1327	95	below_threshold
Labilibaculum filiforme	strain=59.16B	GCA_002843315.1	1940526	1940526	type	True	77.5145	221	1327	95	below_threshold
Carboxylicivirga marina	strain=N1Y132	GCA_016612505.1	2800988	2800988	type	True	76.4523	53	1327	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:36:53,862] [INFO] DFAST Taxonomy check result was written to GCF_004217115.1_ASM421711v1_genomic.fna/tc_result.tsv
[2024-01-24 12:36:53,862] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:36:53,862] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:36:53,862] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg99f5f884-32fb-4627-ac5a-d75d6d035310/dqc_reference/checkm_data
[2024-01-24 12:36:53,864] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:36:53,903] [INFO] Task started: CheckM
[2024-01-24 12:36:53,903] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004217115.1_ASM421711v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004217115.1_ASM421711v1_genomic.fna/checkm_input GCF_004217115.1_ASM421711v1_genomic.fna/checkm_result
[2024-01-24 12:37:43,468] [INFO] Task succeeded: CheckM
[2024-01-24 12:37:43,469] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:37:43,490] [INFO] ===== Completeness check finished =====
[2024-01-24 12:37:43,490] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:37:43,491] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004217115.1_ASM421711v1_genomic.fna/markers.fasta)
[2024-01-24 12:37:43,491] [INFO] Task started: Blastn
[2024-01-24 12:37:43,491] [INFO] Running command: blastn -query GCF_004217115.1_ASM421711v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg99f5f884-32fb-4627-ac5a-d75d6d035310/dqc_reference/reference_markers_gtdb.fasta -out GCF_004217115.1_ASM421711v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:44,282] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:44,286] [INFO] Selected 9 target genomes.
[2024-01-24 12:37:44,286] [INFO] Target genome list was writen to GCF_004217115.1_ASM421711v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:37:44,296] [INFO] Task started: fastANI
[2024-01-24 12:37:44,296] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b11c60f-0fe2-401b-b815-1a28d153bb64/GCF_004217115.1_ASM421711v1_genomic.fna.gz --refList GCF_004217115.1_ASM421711v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004217115.1_ASM421711v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:37:52,416] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:52,431] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:37:52,432] [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_004217115.1	s__Ancylomarina subtilis	100.0	1327	1327	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Ancylomarina	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004122035.1	s__Ancylomarina salipaludis	88.4386	1111	1327	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Ancylomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003863355.1	s__Ancylomarina euxinus	81.9486	868	1327	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Ancylomarina	95.0	99.99	99.99	0.99	0.99	2	-
GCA_016744515.1	s__Ancylomarina sp016744515	80.7694	600	1327	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Ancylomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009669305.1	s__Ancylomarina sp009669305	79.8861	554	1327	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Ancylomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003202155.1	s__Marinifilum breve	78.1241	241	1327	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Marinifilum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610555.1	s__Marinifilum flexuosum	77.9517	246	1327	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Marinifilum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001310955.1	s__Marinifilum fragile	77.893	245	1327	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Marinifilum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016612505.1	s__Carboxylicivirga sp016612505	76.4523	53	1327	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Carboxylicivirga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:37:52,434] [INFO] GTDB search result was written to GCF_004217115.1_ASM421711v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:37:52,435] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:37:52,438] [INFO] DFAST_QC result json was written to GCF_004217115.1_ASM421711v1_genomic.fna/dqc_result.json
[2024-01-24 12:37:52,438] [INFO] DFAST_QC completed!
[2024-01-24 12:37:52,438] [INFO] Total running time: 0h1m28s