[2024-01-24 14:19:34,835] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:34,837] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:34,837] [INFO] DQC Reference Directory: /var/lib/cwl/stg237f1c73-d6b9-4109-8619-10653837c14d/dqc_reference
[2024-01-24 14:19:36,249] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:36,250] [INFO] Task started: Prodigal
[2024-01-24 14:19:36,250] [INFO] Running command: gunzip -c /var/lib/cwl/stg89d1d995-905f-4552-b2d8-cf1180fc283f/GCF_003202155.1_ASM320215v1_genomic.fna.gz | prodigal -d GCF_003202155.1_ASM320215v1_genomic.fna/cds.fna -a GCF_003202155.1_ASM320215v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:01,409] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:01,409] [INFO] Task started: HMMsearch
[2024-01-24 14:20:01,409] [INFO] Running command: hmmsearch --tblout GCF_003202155.1_ASM320215v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg237f1c73-d6b9-4109-8619-10653837c14d/dqc_reference/reference_markers.hmm GCF_003202155.1_ASM320215v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:01,810] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:01,811] [INFO] Found 6/6 markers.
[2024-01-24 14:20:01,864] [INFO] Query marker FASTA was written to GCF_003202155.1_ASM320215v1_genomic.fna/markers.fasta
[2024-01-24 14:20:01,864] [INFO] Task started: Blastn
[2024-01-24 14:20:01,864] [INFO] Running command: blastn -query GCF_003202155.1_ASM320215v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg237f1c73-d6b9-4109-8619-10653837c14d/dqc_reference/reference_markers.fasta -out GCF_003202155.1_ASM320215v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:02,537] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:02,540] [INFO] Selected 12 target genomes.
[2024-01-24 14:20:02,541] [INFO] Target genome list was writen to GCF_003202155.1_ASM320215v1_genomic.fna/target_genomes.txt
[2024-01-24 14:20:02,548] [INFO] Task started: fastANI
[2024-01-24 14:20:02,548] [INFO] Running command: fastANI --query /var/lib/cwl/stg89d1d995-905f-4552-b2d8-cf1180fc283f/GCF_003202155.1_ASM320215v1_genomic.fna.gz --refList GCF_003202155.1_ASM320215v1_genomic.fna/target_genomes.txt --output GCF_003202155.1_ASM320215v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:14,249] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:14,250] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg237f1c73-d6b9-4109-8619-10653837c14d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:14,250] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg237f1c73-d6b9-4109-8619-10653837c14d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:14,260] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:20:14,260] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:14,260] [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
Marinifilum breve	strain=JC075	GCA_003202155.1	2184082	2184082	type	True	100.0	1821	1822	95	conclusive
Marinifilum flexuosum	strain=DSM 21950	GCA_003610555.1	1117708	1117708	type	True	91.2993	1428	1822	95	below_threshold
Marinifilum fragile	strain=JCM 15579	GCA_001310955.1	570161	570161	type	True	87.9718	1259	1822	95	below_threshold
Marinifilum caeruleilacunae	strain=JC070	GCA_013141825.1	2499076	2499076	type	True	82.45	1039	1822	95	below_threshold
Ancylomarina longa	strain=T3-2 S1-C	GCA_003996985.1	2487017	2487017	type	True	78.0248	356	1822	95	below_threshold
Ancylomarina subtilis	strain=DSM 28825	GCA_004217115.1	1639035	1639035	type	True	77.9292	241	1822	95	below_threshold
Labilibaculum manganireducens	strain=59.10-2M	GCA_002843385.1	1940525	1940525	type	True	77.8222	414	1822	95	below_threshold
Labilibaculum filiforme	strain=59.16B	GCA_002843315.1	1940526	1940526	type	True	77.719	434	1822	95	below_threshold
Labilibaculum antarcticum	strain=SPP2	GCA_002356295.1	1717717	1717717	type	True	77.6415	415	1822	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:14,266] [INFO] DFAST Taxonomy check result was written to GCF_003202155.1_ASM320215v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:14,271] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:14,272] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:14,272] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg237f1c73-d6b9-4109-8619-10653837c14d/dqc_reference/checkm_data
[2024-01-24 14:20:14,274] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:14,340] [INFO] Task started: CheckM
[2024-01-24 14:20:14,340] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003202155.1_ASM320215v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003202155.1_ASM320215v1_genomic.fna/checkm_input GCF_003202155.1_ASM320215v1_genomic.fna/checkm_result
[2024-01-24 14:21:24,402] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:24,404] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.47%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:24,429] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:24,430] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:24,430] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003202155.1_ASM320215v1_genomic.fna/markers.fasta)
[2024-01-24 14:21:24,431] [INFO] Task started: Blastn
[2024-01-24 14:21:24,431] [INFO] Running command: blastn -query GCF_003202155.1_ASM320215v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg237f1c73-d6b9-4109-8619-10653837c14d/dqc_reference/reference_markers_gtdb.fasta -out GCF_003202155.1_ASM320215v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:25,256] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:25,259] [INFO] Selected 7 target genomes.
[2024-01-24 14:21:25,259] [INFO] Target genome list was writen to GCF_003202155.1_ASM320215v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:25,274] [INFO] Task started: fastANI
[2024-01-24 14:21:25,275] [INFO] Running command: fastANI --query /var/lib/cwl/stg89d1d995-905f-4552-b2d8-cf1180fc283f/GCF_003202155.1_ASM320215v1_genomic.fna.gz --refList GCF_003202155.1_ASM320215v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003202155.1_ASM320215v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:33,575] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:33,588] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:33,588] [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_003202155.1	s__Marinifilum breve	100.0	1821	1822	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Marinifilum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003610555.1	s__Marinifilum flexuosum	91.2993	1428	1822	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	87.9824	1258	1822	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Marinifilum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013141825.1	s__Marinifilum sp013141825	82.4447	1040	1822	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Marinifilum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009295825.1	s__Marinifilum sp009295825	79.6552	756	1822	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Marinifilum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002843315.1	s__Labilibaculum filiforme	77.7206	435	1822	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 14:21:33,590] [INFO] GTDB search result was written to GCF_003202155.1_ASM320215v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:33,590] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:33,593] [INFO] DFAST_QC result json was written to GCF_003202155.1_ASM320215v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:33,593] [INFO] DFAST_QC completed!
[2024-01-24 14:21:33,593] [INFO] Total running time: 0h1m59s