[2024-01-24 12:40:07,099] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:07,105] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:07,106] [INFO] DQC Reference Directory: /var/lib/cwl/stge14c6bab-2b98-4e02-887b-c8e895115c7d/dqc_reference
[2024-01-24 12:40:08,443] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:08,444] [INFO] Task started: Prodigal
[2024-01-24 12:40:08,444] [INFO] Running command: gunzip -c /var/lib/cwl/stg6b274cf8-637e-4b62-ad88-9cb700f7f85e/GCF_003054005.1_ASM305400v1_genomic.fna.gz | prodigal -d GCF_003054005.1_ASM305400v1_genomic.fna/cds.fna -a GCF_003054005.1_ASM305400v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:22,930] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:22,931] [INFO] Task started: HMMsearch
[2024-01-24 12:40:22,931] [INFO] Running command: hmmsearch --tblout GCF_003054005.1_ASM305400v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge14c6bab-2b98-4e02-887b-c8e895115c7d/dqc_reference/reference_markers.hmm GCF_003054005.1_ASM305400v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:23,264] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:23,266] [INFO] Found 6/6 markers.
[2024-01-24 12:40:23,318] [INFO] Query marker FASTA was written to GCF_003054005.1_ASM305400v1_genomic.fna/markers.fasta
[2024-01-24 12:40:23,319] [INFO] Task started: Blastn
[2024-01-24 12:40:23,319] [INFO] Running command: blastn -query GCF_003054005.1_ASM305400v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge14c6bab-2b98-4e02-887b-c8e895115c7d/dqc_reference/reference_markers.fasta -out GCF_003054005.1_ASM305400v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:24,551] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:24,554] [INFO] Selected 17 target genomes.
[2024-01-24 12:40:24,555] [INFO] Target genome list was writen to GCF_003054005.1_ASM305400v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:24,560] [INFO] Task started: fastANI
[2024-01-24 12:40:24,560] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b274cf8-637e-4b62-ad88-9cb700f7f85e/GCF_003054005.1_ASM305400v1_genomic.fna.gz --refList GCF_003054005.1_ASM305400v1_genomic.fna/target_genomes.txt --output GCF_003054005.1_ASM305400v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:41,475] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:41,476] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge14c6bab-2b98-4e02-887b-c8e895115c7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:41,476] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge14c6bab-2b98-4e02-887b-c8e895115c7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:41,494] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:40:41,494] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:41,495] [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
Pararhodobacter aggregans	strain=DSM 18938	GCA_003054005.1	404875	404875	type	True	100.0	1674	1676	95	conclusive
Pararhodobacter aggregans	strain=D1-19	GCA_003075525.1	404875	404875	type	True	99.9982	1670	1676	95	conclusive
Pararhodobacter marinus	strain=CIC4N-9	GCA_003122215.1	2184063	2184063	type	True	83.118	1055	1676	95	below_threshold
Pararhodobacter zhoushanensis	strain=ZQ420	GCA_003990445.1	2479545	2479545	type	True	81.7065	998	1676	95	below_threshold
Rhodobacter calidifons	strain=M37P	GCA_011174775.1	2715277	2715277	type	True	78.6508	514	1676	95	below_threshold
Rhodovulum visakhapatnamense	strain=JA181	GCA_004365965.1	364297	364297	type	True	78.6424	576	1676	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.6161	526	1676	95	below_threshold
Gemmobacter nectariphilus	strain=DSM 15620	GCA_000429765.1	220343	220343	type	True	78.5838	570	1676	95	below_threshold
Allgaiera indica	strain=CGMCC 1.10859	GCA_014653075.1	765699	765699	type	True	78.4568	546	1676	95	below_threshold
Allgaiera indica	strain=DSM 24802	GCA_900106675.1	765699	765699	type	True	78.4299	551	1676	95	below_threshold
Gemmobacter lanyuensis	strain=KCTC 23714	GCA_014652355.1	1054497	1054497	type	True	78.3616	461	1676	95	below_threshold
Rhabdonatronobacter sediminivivens	strain=IM2376	GCA_013415485.1	2743469	2743469	type	True	78.2601	486	1676	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	78.2534	497	1676	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	78.0711	410	1676	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	78.0156	533	1676	95	below_threshold
Yangia pacifica	strain=CGMCC 1.3455	GCA_900100725.1	311180	311180	suspected-type	True	78.0042	528	1676	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.9773	397	1676	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:41,496] [INFO] DFAST Taxonomy check result was written to GCF_003054005.1_ASM305400v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:41,497] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:41,497] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:41,497] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge14c6bab-2b98-4e02-887b-c8e895115c7d/dqc_reference/checkm_data
[2024-01-24 12:40:41,498] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:41,545] [INFO] Task started: CheckM
[2024-01-24 12:40:41,545] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003054005.1_ASM305400v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003054005.1_ASM305400v1_genomic.fna/checkm_input GCF_003054005.1_ASM305400v1_genomic.fna/checkm_result
[2024-01-24 12:41:32,507] [INFO] Task succeeded: CheckM
[2024-01-24 12:41:32,509] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:41:32,531] [INFO] ===== Completeness check finished =====
[2024-01-24 12:41:32,532] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:41:32,532] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003054005.1_ASM305400v1_genomic.fna/markers.fasta)
[2024-01-24 12:41:32,532] [INFO] Task started: Blastn
[2024-01-24 12:41:32,533] [INFO] Running command: blastn -query GCF_003054005.1_ASM305400v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge14c6bab-2b98-4e02-887b-c8e895115c7d/dqc_reference/reference_markers_gtdb.fasta -out GCF_003054005.1_ASM305400v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:34,659] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:34,664] [INFO] Selected 8 target genomes.
[2024-01-24 12:41:34,664] [INFO] Target genome list was writen to GCF_003054005.1_ASM305400v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:41:34,670] [INFO] Task started: fastANI
[2024-01-24 12:41:34,671] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b274cf8-637e-4b62-ad88-9cb700f7f85e/GCF_003054005.1_ASM305400v1_genomic.fna.gz --refList GCF_003054005.1_ASM305400v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003054005.1_ASM305400v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:43,662] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:43,674] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:41:43,674] [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_003075525.1	s__Pararhodobacter aggregans	99.9982	1670	1676	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_001691415.1	s__Pararhodobacter sp001691415	83.4593	1054	1676	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003122215.1	s__Pararhodobacter marinus	83.1015	1057	1676	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017303295.1	s__Pararhodobacter sp017303295	82.3187	1040	1676	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003990445.1	s__Pararhodobacter zhoushanensis	81.685	1002	1676	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007131945.1	s__Pararhodobacter sp007131945	79.5216	509	1676	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	99.16	99.15	0.86	0.82	3	-
GCA_001314715.1	s__Pararhodobacter sp001314715	78.9607	571	1676	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007134405.1	s__Pararhodobacter sp007134405	78.8029	356	1676	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	98.66	98.61	0.77	0.76	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:41:43,676] [INFO] GTDB search result was written to GCF_003054005.1_ASM305400v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:43,678] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:43,684] [INFO] DFAST_QC result json was written to GCF_003054005.1_ASM305400v1_genomic.fna/dqc_result.json
[2024-01-24 12:41:43,685] [INFO] DFAST_QC completed!
[2024-01-24 12:41:43,685] [INFO] Total running time: 0h1m37s