[2024-01-24 12:37:09,125] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:09,261] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:09,262] [INFO] DQC Reference Directory: /var/lib/cwl/stgef2674b8-5127-413d-9cd4-0e2e448af69f/dqc_reference
[2024-01-24 12:37:10,557] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:10,559] [INFO] Task started: Prodigal
[2024-01-24 12:37:10,560] [INFO] Running command: gunzip -c /var/lib/cwl/stg68c44d03-f9e5-42dd-a457-4d6d517b152d/GCF_003121985.1_ASM312198v1_genomic.fna.gz | prodigal -d GCF_003121985.1_ASM312198v1_genomic.fna/cds.fna -a GCF_003121985.1_ASM312198v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:35,000] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:35,001] [INFO] Task started: HMMsearch
[2024-01-24 12:37:35,001] [INFO] Running command: hmmsearch --tblout GCF_003121985.1_ASM312198v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgef2674b8-5127-413d-9cd4-0e2e448af69f/dqc_reference/reference_markers.hmm GCF_003121985.1_ASM312198v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:35,312] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:35,314] [INFO] Found 6/6 markers.
[2024-01-24 12:37:35,358] [INFO] Query marker FASTA was written to GCF_003121985.1_ASM312198v1_genomic.fna/markers.fasta
[2024-01-24 12:37:35,359] [INFO] Task started: Blastn
[2024-01-24 12:37:35,359] [INFO] Running command: blastn -query GCF_003121985.1_ASM312198v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgef2674b8-5127-413d-9cd4-0e2e448af69f/dqc_reference/reference_markers.fasta -out GCF_003121985.1_ASM312198v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:35,957] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:35,962] [INFO] Selected 17 target genomes.
[2024-01-24 12:37:35,962] [INFO] Target genome list was writen to GCF_003121985.1_ASM312198v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:35,978] [INFO] Task started: fastANI
[2024-01-24 12:37:35,978] [INFO] Running command: fastANI --query /var/lib/cwl/stg68c44d03-f9e5-42dd-a457-4d6d517b152d/GCF_003121985.1_ASM312198v1_genomic.fna.gz --refList GCF_003121985.1_ASM312198v1_genomic.fna/target_genomes.txt --output GCF_003121985.1_ASM312198v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:50,795] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:50,796] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgef2674b8-5127-413d-9cd4-0e2e448af69f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:50,796] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgef2674b8-5127-413d-9cd4-0e2e448af69f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:50,807] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:37:50,807] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:50,807] [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
Marinilabilia rubra	strain=WTE16	GCA_003121985.1	2162893	2162893	type	True	100.0	1762	1763	95	conclusive
Marinilabilia salmonicolor	strain=JCM 21150	GCA_000259075.1	989	989	type	True	78.7007	385	1763	95	below_threshold
Marinilabilia salmonicolor	strain=JCM 21150	GCA_000614895.1	989	989	type	True	78.6003	389	1763	95	below_threshold
Anaerophaga thermohalophila	strain=DSM 12881	GCA_000191885.2	177400	177400	type	True	77.4724	244	1763	95	below_threshold
Thermophagus xiamenensis	strain=HS1	GCA_000220155.2	385682	385682	type	True	76.8481	128	1763	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:50,809] [INFO] DFAST Taxonomy check result was written to GCF_003121985.1_ASM312198v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:50,810] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:50,810] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:50,810] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgef2674b8-5127-413d-9cd4-0e2e448af69f/dqc_reference/checkm_data
[2024-01-24 12:37:50,811] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:50,865] [INFO] Task started: CheckM
[2024-01-24 12:37:50,865] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003121985.1_ASM312198v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003121985.1_ASM312198v1_genomic.fna/checkm_input GCF_003121985.1_ASM312198v1_genomic.fna/checkm_result
[2024-01-24 12:39:01,704] [INFO] Task succeeded: CheckM
[2024-01-24 12:39:01,706] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:39:01,738] [INFO] ===== Completeness check finished =====
[2024-01-24 12:39:01,739] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:39:01,739] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003121985.1_ASM312198v1_genomic.fna/markers.fasta)
[2024-01-24 12:39:01,739] [INFO] Task started: Blastn
[2024-01-24 12:39:01,740] [INFO] Running command: blastn -query GCF_003121985.1_ASM312198v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgef2674b8-5127-413d-9cd4-0e2e448af69f/dqc_reference/reference_markers_gtdb.fasta -out GCF_003121985.1_ASM312198v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:39:02,531] [INFO] Task succeeded: Blastn
[2024-01-24 12:39:02,535] [INFO] Selected 16 target genomes.
[2024-01-24 12:39:02,535] [INFO] Target genome list was writen to GCF_003121985.1_ASM312198v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:39:02,556] [INFO] Task started: fastANI
[2024-01-24 12:39:02,556] [INFO] Running command: fastANI --query /var/lib/cwl/stg68c44d03-f9e5-42dd-a457-4d6d517b152d/GCF_003121985.1_ASM312198v1_genomic.fna.gz --refList GCF_003121985.1_ASM312198v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003121985.1_ASM312198v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:39:19,003] [INFO] Task succeeded: fastANI
[2024-01-24 12:39:19,018] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:39:19,018] [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_003121985.1	s__Marinilabilia rubra	100.0	1762	1763	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Marinilabilia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003003035.1	s__Marinilabilia salmonicolor_A	78.7536	406	1763	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Marinilabilia	95.0	98.82	98.82	0.92	0.92	2	-
GCF_000259075.1	s__Marinilabilia salmonicolor	78.7455	385	1763	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Marinilabilia	95.0	99.96	99.96	0.99	0.99	2	-
GCA_002411085.1	s__Marinilabilia sp002411085	78.4064	318	1763	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	78.029	300	1763	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Marinilabilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000191885.1	s__Anaerophaga thermohalophila	77.4749	243	1763	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Anaerophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000250735.1	s__Anaerophaga thermohalophila_A	77.1706	255	1763	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Anaerophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345615.1	s__Natronoflexus pectinivorans	76.408	63	1763	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Natronoflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004296775.1	s__JC017 sp004296775	76.2197	70	1763	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__JC017	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:39:19,020] [INFO] GTDB search result was written to GCF_003121985.1_ASM312198v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:39:19,021] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:39:19,024] [INFO] DFAST_QC result json was written to GCF_003121985.1_ASM312198v1_genomic.fna/dqc_result.json
[2024-01-24 12:39:19,025] [INFO] DFAST_QC completed!
[2024-01-24 12:39:19,025] [INFO] Total running time: 0h2m10s