[2024-01-24 13:56:12,395] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:56:12,399] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:56:12,399] [INFO] DQC Reference Directory: /var/lib/cwl/stg1b2643d8-e53e-4196-b469-4438b7ecf0d3/dqc_reference
[2024-01-24 13:56:14,423] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:56:14,424] [INFO] Task started: Prodigal
[2024-01-24 13:56:14,425] [INFO] Running command: gunzip -c /var/lib/cwl/stgde2f9121-3698-4d39-bdb2-c40aa6986106/GCF_014652915.1_ASM1465291v1_genomic.fna.gz | prodigal -d GCF_014652915.1_ASM1465291v1_genomic.fna/cds.fna -a GCF_014652915.1_ASM1465291v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:30,627] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:30,628] [INFO] Task started: HMMsearch
[2024-01-24 13:56:30,628] [INFO] Running command: hmmsearch --tblout GCF_014652915.1_ASM1465291v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1b2643d8-e53e-4196-b469-4438b7ecf0d3/dqc_reference/reference_markers.hmm GCF_014652915.1_ASM1465291v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:30,975] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:30,977] [INFO] Found 6/6 markers.
[2024-01-24 13:56:31,032] [INFO] Query marker FASTA was written to GCF_014652915.1_ASM1465291v1_genomic.fna/markers.fasta
[2024-01-24 13:56:31,032] [INFO] Task started: Blastn
[2024-01-24 13:56:31,033] [INFO] Running command: blastn -query GCF_014652915.1_ASM1465291v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b2643d8-e53e-4196-b469-4438b7ecf0d3/dqc_reference/reference_markers.fasta -out GCF_014652915.1_ASM1465291v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:32,143] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:32,146] [INFO] Selected 20 target genomes.
[2024-01-24 13:56:32,147] [INFO] Target genome list was writen to GCF_014652915.1_ASM1465291v1_genomic.fna/target_genomes.txt
[2024-01-24 13:56:32,157] [INFO] Task started: fastANI
[2024-01-24 13:56:32,157] [INFO] Running command: fastANI --query /var/lib/cwl/stgde2f9121-3698-4d39-bdb2-c40aa6986106/GCF_014652915.1_ASM1465291v1_genomic.fna.gz --refList GCF_014652915.1_ASM1465291v1_genomic.fna/target_genomes.txt --output GCF_014652915.1_ASM1465291v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:55,570] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:55,572] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1b2643d8-e53e-4196-b469-4438b7ecf0d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:55,572] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1b2643d8-e53e-4196-b469-4438b7ecf0d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:55,595] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:56:55,595] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:55,595] [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
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	100.0	1974	1975	95	conclusive
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	78.5616	518	1975	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	78.0889	817	1975	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	78.0759	813	1975	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	77.9372	495	1975	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	77.8042	431	1975	95	below_threshold
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	77.6747	425	1975	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	77.6699	391	1975	95	below_threshold
Rhodovibrio sodomensis	strain=DSM 9895	GCA_016583645.1	1088	1088	type	True	77.54	488	1975	95	below_threshold
Azospirillum soli	strain=CC-LY788	GCA_017876165.1	1304799	1304799	type	True	77.2047	480	1975	95	below_threshold
Azospirillum thermophilum	strain=CFH 70021	GCA_003130795.1	2202148	2202148	type	True	77.1962	629	1975	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	77.1482	667	1975	95	below_threshold
Azospirillum rugosum	strain=IMMIB AFH-6	GCA_017876155.1	416170	416170	type	True	77.1091	587	1975	95	below_threshold
Azospirillum oleiclasticum	strain=RWY-5-1-1	GCA_013423485.1	2735135	2735135	type	True	77.0026	604	1975	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	76.9255	596	1975	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	76.9166	511	1975	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	76.9104	426	1975	95	below_threshold
Pararhodospirillum oryzae	strain=NBRC 107573	GCA_007992075.1	478448	478448	type	True	76.7119	224	1975	95	below_threshold
Roseomonas alkaliterrae	strain=DSM 25895	GCA_014199195.1	1452450	1452450	type	True	76.4902	439	1975	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	76.2991	591	1975	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:55,597] [INFO] DFAST Taxonomy check result was written to GCF_014652915.1_ASM1465291v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:55,598] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:55,598] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:55,598] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1b2643d8-e53e-4196-b469-4438b7ecf0d3/dqc_reference/checkm_data
[2024-01-24 13:56:55,600] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:55,666] [INFO] Task started: CheckM
[2024-01-24 13:56:55,666] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014652915.1_ASM1465291v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014652915.1_ASM1465291v1_genomic.fna/checkm_input GCF_014652915.1_ASM1465291v1_genomic.fna/checkm_result
[2024-01-24 13:57:48,222] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:48,224] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:48,255] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:48,256] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:48,256] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014652915.1_ASM1465291v1_genomic.fna/markers.fasta)
[2024-01-24 13:57:48,257] [INFO] Task started: Blastn
[2024-01-24 13:57:48,257] [INFO] Running command: blastn -query GCF_014652915.1_ASM1465291v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b2643d8-e53e-4196-b469-4438b7ecf0d3/dqc_reference/reference_markers_gtdb.fasta -out GCF_014652915.1_ASM1465291v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:50,542] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:50,546] [INFO] Selected 9 target genomes.
[2024-01-24 13:57:50,546] [INFO] Target genome list was writen to GCF_014652915.1_ASM1465291v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:50,588] [INFO] Task started: fastANI
[2024-01-24 13:57:50,589] [INFO] Running command: fastANI --query /var/lib/cwl/stgde2f9121-3698-4d39-bdb2-c40aa6986106/GCF_014652915.1_ASM1465291v1_genomic.fna.gz --refList GCF_014652915.1_ASM1465291v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014652915.1_ASM1465291v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:03,922] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:03,933] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:03,933] [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_014652915.1	s__Thalassobaculum_A fulvum	100.0	1974	1975	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018401495.1	s__Thalassobaculum_A sp018401495	84.4473	1254	1975	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000171835.1	s__Thalassobaculum_A sp000171835	82.3261	1259	1975	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102465.1	s__Thalassobaculum litoreum	80.6216	970	1975	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum	95.0	98.83	98.83	0.96	0.96	2	-
GCA_013203465.1	s__JABMNR01 sp013203465	79.5408	760	1975	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__JABMNR01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177295.1	s__Tistlia consotensis	78.022	829	1975	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Tistlia	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003116015.1	s__Azospirillum sp003116015	77.4766	674	1975	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016699855.1	s__GCA-016699855 sp016699855	77.1622	597	1975	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__GCA-016699855	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576685.1	s__SYSU-D60014 sp003576685	76.8435	363	1975	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__SYSU-D60014	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:03,936] [INFO] GTDB search result was written to GCF_014652915.1_ASM1465291v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:03,937] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:03,941] [INFO] DFAST_QC result json was written to GCF_014652915.1_ASM1465291v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:03,941] [INFO] DFAST_QC completed!
[2024-01-24 13:58:03,941] [INFO] Total running time: 0h1m52s