[2024-01-24 12:05:26,611] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:05:26,615] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:05:26,615] [INFO] DQC Reference Directory: /var/lib/cwl/stg852e601e-e625-4159-a9ab-8a5401bd9e6c/dqc_reference
[2024-01-24 12:05:30,676] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:05:30,678] [INFO] Task started: Prodigal
[2024-01-24 12:05:30,678] [INFO] Running command: gunzip -c /var/lib/cwl/stgb4eb9eac-108e-4270-9146-a0e3d33c1314/GCF_002356295.1_ASM235629v1_genomic.fna.gz | prodigal -d GCF_002356295.1_ASM235629v1_genomic.fna/cds.fna -a GCF_002356295.1_ASM235629v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:05:53,704] [INFO] Task succeeded: Prodigal
[2024-01-24 12:05:53,705] [INFO] Task started: HMMsearch
[2024-01-24 12:05:53,705] [INFO] Running command: hmmsearch --tblout GCF_002356295.1_ASM235629v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg852e601e-e625-4159-a9ab-8a5401bd9e6c/dqc_reference/reference_markers.hmm GCF_002356295.1_ASM235629v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:05:54,031] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:05:54,033] [INFO] Found 6/6 markers.
[2024-01-24 12:05:54,078] [INFO] Query marker FASTA was written to GCF_002356295.1_ASM235629v1_genomic.fna/markers.fasta
[2024-01-24 12:05:54,078] [INFO] Task started: Blastn
[2024-01-24 12:05:54,078] [INFO] Running command: blastn -query GCF_002356295.1_ASM235629v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg852e601e-e625-4159-a9ab-8a5401bd9e6c/dqc_reference/reference_markers.fasta -out GCF_002356295.1_ASM235629v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:05:54,698] [INFO] Task succeeded: Blastn
[2024-01-24 12:05:54,701] [INFO] Selected 14 target genomes.
[2024-01-24 12:05:54,702] [INFO] Target genome list was writen to GCF_002356295.1_ASM235629v1_genomic.fna/target_genomes.txt
[2024-01-24 12:05:54,714] [INFO] Task started: fastANI
[2024-01-24 12:05:54,714] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4eb9eac-108e-4270-9146-a0e3d33c1314/GCF_002356295.1_ASM235629v1_genomic.fna.gz --refList GCF_002356295.1_ASM235629v1_genomic.fna/target_genomes.txt --output GCF_002356295.1_ASM235629v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:08,175] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:08,175] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg852e601e-e625-4159-a9ab-8a5401bd9e6c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:08,176] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg852e601e-e625-4159-a9ab-8a5401bd9e6c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:08,185] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:08,185] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:08,185] [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
Labilibaculum antarcticum	strain=SPP2	GCA_002356295.1	1717717	1717717	type	True	100.0	1902	1906	95	conclusive
Labilibaculum manganireducens	strain=59.10-2M	GCA_002843385.1	1940525	1940525	type	True	84.2127	1139	1906	95	below_threshold
Labilibaculum filiforme	strain=59.16B	GCA_002843315.1	1940526	1940526	type	True	81.561	1106	1906	95	below_threshold
Marinifilum breve	strain=JC075	GCA_003202155.1	2184082	2184082	type	True	77.8956	403	1906	95	below_threshold
Marinifilum flexuosum	strain=DSM 21950	GCA_003610555.1	1117708	1117708	type	True	77.889	430	1906	95	below_threshold
Marinifilum fragile	strain=JCM 15579	GCA_001310955.1	570161	570161	type	True	77.7746	414	1906	95	below_threshold
Ancylomarina longa	strain=T3-2 S1-C	GCA_003996985.1	2487017	2487017	type	True	77.5687	424	1906	95	below_threshold
Marinifilum caeruleilacunae	strain=JC070	GCA_013141825.1	2499076	2499076	type	True	77.5444	425	1906	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	76.4828	57	1906	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:08,187] [INFO] DFAST Taxonomy check result was written to GCF_002356295.1_ASM235629v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:08,187] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:08,187] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:08,187] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg852e601e-e625-4159-a9ab-8a5401bd9e6c/dqc_reference/checkm_data
[2024-01-24 12:06:08,188] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:08,242] [INFO] Task started: CheckM
[2024-01-24 12:06:08,242] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002356295.1_ASM235629v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002356295.1_ASM235629v1_genomic.fna/checkm_input GCF_002356295.1_ASM235629v1_genomic.fna/checkm_result
[2024-01-24 12:07:13,380] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:13,381] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:13,406] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:13,406] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:13,406] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002356295.1_ASM235629v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:13,407] [INFO] Task started: Blastn
[2024-01-24 12:07:13,407] [INFO] Running command: blastn -query GCF_002356295.1_ASM235629v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg852e601e-e625-4159-a9ab-8a5401bd9e6c/dqc_reference/reference_markers_gtdb.fasta -out GCF_002356295.1_ASM235629v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:14,226] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:14,233] [INFO] Selected 7 target genomes.
[2024-01-24 12:07:14,233] [INFO] Target genome list was writen to GCF_002356295.1_ASM235629v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:14,241] [INFO] Task started: fastANI
[2024-01-24 12:07:14,242] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4eb9eac-108e-4270-9146-a0e3d33c1314/GCF_002356295.1_ASM235629v1_genomic.fna.gz --refList GCF_002356295.1_ASM235629v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002356295.1_ASM235629v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:23,082] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:23,089] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:23,090] [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_002356295.1	s__Labilibaculum antarcticum	100.0	1904	1906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Labilibaculum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016760525.1	s__Labilibaculum sp016760525	85.2039	558	1906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Labilibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009795715.1	s__Labilibaculum euxinus	84.5751	1151	1906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Labilibaculum	95.0	97.85	97.85	0.89	0.89	3	-
GCA_016936255.1	s__Labilibaculum sp016936255	84.4432	1098	1906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Labilibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002843385.1	s__Labilibaculum manganireducens	84.2326	1137	1906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Labilibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002843315.1	s__Labilibaculum filiforme	81.5707	1104	1906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Labilibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016342745.1	s__Labilibaculum sp016342745	80.4643	895	1906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Labilibaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:23,091] [INFO] GTDB search result was written to GCF_002356295.1_ASM235629v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:23,092] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:23,095] [INFO] DFAST_QC result json was written to GCF_002356295.1_ASM235629v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:23,095] [INFO] DFAST_QC completed!
[2024-01-24 12:07:23,095] [INFO] Total running time: 0h1m56s