[2024-01-24 13:46:18,314] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:18,318] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:18,318] [INFO] DQC Reference Directory: /var/lib/cwl/stg3377bf50-c5ec-49ca-9a6f-98f1c1ae4c9b/dqc_reference
[2024-01-24 13:46:19,684] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:19,690] [INFO] Task started: Prodigal
[2024-01-24 13:46:19,691] [INFO] Running command: gunzip -c /var/lib/cwl/stg8b36104e-b366-45c0-8536-d94fc911c646/GCF_000191885.1_ASM19188v1_genomic.fna.gz | prodigal -d GCF_000191885.1_ASM19188v1_genomic.fna/cds.fna -a GCF_000191885.1_ASM19188v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:40,069] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:40,070] [INFO] Task started: HMMsearch
[2024-01-24 13:46:40,070] [INFO] Running command: hmmsearch --tblout GCF_000191885.1_ASM19188v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3377bf50-c5ec-49ca-9a6f-98f1c1ae4c9b/dqc_reference/reference_markers.hmm GCF_000191885.1_ASM19188v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:40,402] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:40,404] [INFO] Found 6/6 markers.
[2024-01-24 13:46:40,441] [INFO] Query marker FASTA was written to GCF_000191885.1_ASM19188v1_genomic.fna/markers.fasta
[2024-01-24 13:46:40,441] [INFO] Task started: Blastn
[2024-01-24 13:46:40,442] [INFO] Running command: blastn -query GCF_000191885.1_ASM19188v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3377bf50-c5ec-49ca-9a6f-98f1c1ae4c9b/dqc_reference/reference_markers.fasta -out GCF_000191885.1_ASM19188v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:41,070] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:41,074] [INFO] Selected 18 target genomes.
[2024-01-24 13:46:41,075] [INFO] Target genome list was writen to GCF_000191885.1_ASM19188v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:41,088] [INFO] Task started: fastANI
[2024-01-24 13:46:41,088] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b36104e-b366-45c0-8536-d94fc911c646/GCF_000191885.1_ASM19188v1_genomic.fna.gz --refList GCF_000191885.1_ASM19188v1_genomic.fna/target_genomes.txt --output GCF_000191885.1_ASM19188v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:00,332] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:00,332] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3377bf50-c5ec-49ca-9a6f-98f1c1ae4c9b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:00,332] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3377bf50-c5ec-49ca-9a6f-98f1c1ae4c9b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:00,339] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:47:00,340] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:47:00,340] [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
Anaerophaga thermohalophila	strain=DSM 12881	GCA_000191885.2	177400	177400	type	True	100.0	1318	1353	95	conclusive
Marinilabilia rubra	strain=WTE16	GCA_003121985.1	2162893	2162893	type	True	77.5262	234	1353	95	below_threshold
Marinilabilia salmonicolor	strain=JCM 21150	GCA_000259075.1	989	989	type	True	77.1527	279	1353	95	below_threshold
Marinilabilia salmonicolor	strain=JCM 21150	GCA_000614895.1	989	989	type	True	77.1364	271	1353	95	below_threshold
Thermophagus xiamenensis	strain=DSM 19012	GCA_900112795.1	385682	385682	type	True	76.9193	228	1353	95	below_threshold
Thermophagus xiamenensis	strain=HS1	GCA_000220155.2	385682	385682	type	True	76.8475	217	1353	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:00,341] [INFO] DFAST Taxonomy check result was written to GCF_000191885.1_ASM19188v1_genomic.fna/tc_result.tsv
[2024-01-24 13:47:00,342] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:00,342] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:00,342] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3377bf50-c5ec-49ca-9a6f-98f1c1ae4c9b/dqc_reference/checkm_data
[2024-01-24 13:47:00,343] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:00,387] [INFO] Task started: CheckM
[2024-01-24 13:47:00,387] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000191885.1_ASM19188v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000191885.1_ASM19188v1_genomic.fna/checkm_input GCF_000191885.1_ASM19188v1_genomic.fna/checkm_result
[2024-01-24 13:47:58,414] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:58,415] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:58,444] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:58,444] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:58,445] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000191885.1_ASM19188v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:58,445] [INFO] Task started: Blastn
[2024-01-24 13:47:58,445] [INFO] Running command: blastn -query GCF_000191885.1_ASM19188v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3377bf50-c5ec-49ca-9a6f-98f1c1ae4c9b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000191885.1_ASM19188v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:59,290] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:59,297] [INFO] Selected 15 target genomes.
[2024-01-24 13:47:59,297] [INFO] Target genome list was writen to GCF_000191885.1_ASM19188v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:59,322] [INFO] Task started: fastANI
[2024-01-24 13:47:59,322] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b36104e-b366-45c0-8536-d94fc911c646/GCF_000191885.1_ASM19188v1_genomic.fna.gz --refList GCF_000191885.1_ASM19188v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000191885.1_ASM19188v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:48:16,932] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:16,939] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:48:16,940] [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_000191885.1	s__Anaerophaga thermohalophila	100.0	1320	1353	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Anaerophaga	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000250735.1	s__Anaerophaga thermohalophila_A	90.2674	950	1353	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Anaerophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003035.1	s__Marinilabilia salmonicolor_A	77.63	257	1353	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Marinilabilia	95.0	98.82	98.82	0.92	0.92	2	-
GCF_003121985.1	s__Marinilabilia rubra	77.5854	232	1353	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Marinilabilia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002411085.1	s__Marinilabilia sp002411085	77.5492	203	1353	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Marinilabilia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016278715.1	s__Marinilabilia sp016278715	77.3722	244	1353	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Marinilabilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112795.1	s__Thermophagus xiamenensis	76.927	230	1353	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Thermophagus	95.0	99.97	99.97	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:48:16,941] [INFO] GTDB search result was written to GCF_000191885.1_ASM19188v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:48:16,942] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:48:16,945] [INFO] DFAST_QC result json was written to GCF_000191885.1_ASM19188v1_genomic.fna/dqc_result.json
[2024-01-24 13:48:16,945] [INFO] DFAST_QC completed!
[2024-01-24 13:48:16,945] [INFO] Total running time: 0h1m59s