[2024-01-24 11:58:55,135] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:58:55,137] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:58:55,137] [INFO] DQC Reference Directory: /var/lib/cwl/stg59cebad0-ef36-4c92-bf3a-480ad810b1fb/dqc_reference
[2024-01-24 11:58:56,382] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:58:56,383] [INFO] Task started: Prodigal
[2024-01-24 11:58:56,384] [INFO] Running command: gunzip -c /var/lib/cwl/stg52baf18f-6dc8-46b5-ab96-0ef3d5e8acfc/GCF_019802255.1_ASM1980225v1_genomic.fna.gz | prodigal -d GCF_019802255.1_ASM1980225v1_genomic.fna/cds.fna -a GCF_019802255.1_ASM1980225v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:21,296] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:21,296] [INFO] Task started: HMMsearch
[2024-01-24 11:59:21,297] [INFO] Running command: hmmsearch --tblout GCF_019802255.1_ASM1980225v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg59cebad0-ef36-4c92-bf3a-480ad810b1fb/dqc_reference/reference_markers.hmm GCF_019802255.1_ASM1980225v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:21,683] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:21,684] [INFO] Found 6/6 markers.
[2024-01-24 11:59:21,730] [INFO] Query marker FASTA was written to GCF_019802255.1_ASM1980225v1_genomic.fna/markers.fasta
[2024-01-24 11:59:21,731] [INFO] Task started: Blastn
[2024-01-24 11:59:21,731] [INFO] Running command: blastn -query GCF_019802255.1_ASM1980225v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg59cebad0-ef36-4c92-bf3a-480ad810b1fb/dqc_reference/reference_markers.fasta -out GCF_019802255.1_ASM1980225v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:22,432] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:22,436] [INFO] Selected 15 target genomes.
[2024-01-24 11:59:22,436] [INFO] Target genome list was writen to GCF_019802255.1_ASM1980225v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:22,443] [INFO] Task started: fastANI
[2024-01-24 11:59:22,443] [INFO] Running command: fastANI --query /var/lib/cwl/stg52baf18f-6dc8-46b5-ab96-0ef3d5e8acfc/GCF_019802255.1_ASM1980225v1_genomic.fna.gz --refList GCF_019802255.1_ASM1980225v1_genomic.fna/target_genomes.txt --output GCF_019802255.1_ASM1980225v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:37,750] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:37,750] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg59cebad0-ef36-4c92-bf3a-480ad810b1fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:37,751] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg59cebad0-ef36-4c92-bf3a-480ad810b1fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:37,762] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:59:37,763] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:59:37,763] [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
Pedobacter gandavensis	strain=LMG 31462	GCA_014172405.1	2679963	2679963	type	True	84.8567	1246	1935	95	below_threshold
Pedobacter caeni	strain=DSM 16990	GCA_900129215.1	288992	288992	type	True	81.5351	883	1935	95	below_threshold
Pedobacter steynii	strain=DSM 19110	GCA_900103665.1	430522	430522	type	True	81.1162	834	1935	95	below_threshold
Pedobacter hiemivivus	strain=RP-3-8	GCA_004331685.1	2530454	2530454	type	True	79.3295	439	1935	95	below_threshold
Pedobacter nyackensis	strain=DSM 19625	GCA_900176505.1	475255	475255	type	True	78.8726	420	1935	95	below_threshold
Pedobacter frigoris	strain=RP-3-15	GCA_005116445.1	2571272	2571272	type	True	78.8067	324	1935	95	below_threshold
Pedobacter foliorum	strain=LMG 31463	GCA_013266735.1	2739058	2739058	type	True	78.7515	395	1935	95	below_threshold
Pedobacter panaciterrae	strain=LMG 23400	GCA_013204795.1	363849	363849	type	True	78.6436	393	1935	95	below_threshold
Pedobacter fastidiosus	strain=CCM 8938	GCA_014306625.1	2765361	2765361	type	True	77.664	165	1935	95	below_threshold
Pedobacter miscanthi	strain=RS10	GCA_003315595.1	2259170	2259170	type	True	77.3325	191	1935	95	below_threshold
Pedobacter segetis	strain=SD-b	GCA_016623585.1	2793069	2793069	type	True	77.0123	51	1935	95	below_threshold
Mucilaginibacter conchicola	strain=MYSH2	GCA_003432115.1	2303333	2303333	type	True	76.4096	51	1935	95	below_threshold
Sphingobacterium prati	strain=arapr2	GCA_013167215.1	2737006	2737006	type	True	76.0298	52	1935	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:37,765] [INFO] DFAST Taxonomy check result was written to GCF_019802255.1_ASM1980225v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:37,765] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:37,765] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:37,766] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg59cebad0-ef36-4c92-bf3a-480ad810b1fb/dqc_reference/checkm_data
[2024-01-24 11:59:37,767] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:37,822] [INFO] Task started: CheckM
[2024-01-24 11:59:37,822] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019802255.1_ASM1980225v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019802255.1_ASM1980225v1_genomic.fna/checkm_input GCF_019802255.1_ASM1980225v1_genomic.fna/checkm_result
[2024-01-24 12:00:45,313] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:45,314] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:45,330] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:45,331] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:45,331] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019802255.1_ASM1980225v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:45,331] [INFO] Task started: Blastn
[2024-01-24 12:00:45,331] [INFO] Running command: blastn -query GCF_019802255.1_ASM1980225v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg59cebad0-ef36-4c92-bf3a-480ad810b1fb/dqc_reference/reference_markers_gtdb.fasta -out GCF_019802255.1_ASM1980225v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:46,152] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:46,156] [INFO] Selected 8 target genomes.
[2024-01-24 12:00:46,156] [INFO] Target genome list was writen to GCF_019802255.1_ASM1980225v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:46,162] [INFO] Task started: fastANI
[2024-01-24 12:00:46,162] [INFO] Running command: fastANI --query /var/lib/cwl/stg52baf18f-6dc8-46b5-ab96-0ef3d5e8acfc/GCF_019802255.1_ASM1980225v1_genomic.fna.gz --refList GCF_019802255.1_ASM1980225v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019802255.1_ASM1980225v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:55,325] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:55,332] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:00:55,332] [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_001412655.1	s__Pedobacter sp001412655	92.8414	1638	1935	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014472395.1	s__Pedobacter sp014472395	90.5887	1456	1935	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014172405.1	s__Pedobacter gandavensis	84.8567	1246	1935	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129215.1	s__Pedobacter caeni	81.554	880	1935	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103665.1	s__Pedobacter steynii	81.0973	837	1935	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003852525.1	s__Pedobacter sp003852525	80.9683	877	1935	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:55,334] [INFO] GTDB search result was written to GCF_019802255.1_ASM1980225v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:55,334] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:55,337] [INFO] DFAST_QC result json was written to GCF_019802255.1_ASM1980225v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:55,337] [INFO] DFAST_QC completed!
[2024-01-24 12:00:55,337] [INFO] Total running time: 0h2m0s