[2024-01-25 20:15:05,341] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:15:05,342] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:15:05,343] [INFO] DQC Reference Directory: /var/lib/cwl/stg59c3a267-5b93-4f61-b7a1-5a7fdf6a259c/dqc_reference
[2024-01-25 20:15:06,451] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:15:06,452] [INFO] Task started: Prodigal
[2024-01-25 20:15:06,452] [INFO] Running command: gunzip -c /var/lib/cwl/stgf46ad1d9-747a-4b46-b01a-0b2849a224aa/GCF_020866905.1_ASM2086690v1_genomic.fna.gz | prodigal -d GCF_020866905.1_ASM2086690v1_genomic.fna/cds.fna -a GCF_020866905.1_ASM2086690v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:15:18,894] [INFO] Task succeeded: Prodigal
[2024-01-25 20:15:18,894] [INFO] Task started: HMMsearch
[2024-01-25 20:15:18,895] [INFO] Running command: hmmsearch --tblout GCF_020866905.1_ASM2086690v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg59c3a267-5b93-4f61-b7a1-5a7fdf6a259c/dqc_reference/reference_markers.hmm GCF_020866905.1_ASM2086690v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:15:19,188] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:15:19,189] [INFO] Found 6/6 markers.
[2024-01-25 20:15:19,219] [INFO] Query marker FASTA was written to GCF_020866905.1_ASM2086690v1_genomic.fna/markers.fasta
[2024-01-25 20:15:19,220] [INFO] Task started: Blastn
[2024-01-25 20:15:19,220] [INFO] Running command: blastn -query GCF_020866905.1_ASM2086690v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg59c3a267-5b93-4f61-b7a1-5a7fdf6a259c/dqc_reference/reference_markers.fasta -out GCF_020866905.1_ASM2086690v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:15:19,827] [INFO] Task succeeded: Blastn
[2024-01-25 20:15:19,829] [INFO] Selected 13 target genomes.
[2024-01-25 20:15:19,829] [INFO] Target genome list was writen to GCF_020866905.1_ASM2086690v1_genomic.fna/target_genomes.txt
[2024-01-25 20:15:19,835] [INFO] Task started: fastANI
[2024-01-25 20:15:19,836] [INFO] Running command: fastANI --query /var/lib/cwl/stgf46ad1d9-747a-4b46-b01a-0b2849a224aa/GCF_020866905.1_ASM2086690v1_genomic.fna.gz --refList GCF_020866905.1_ASM2086690v1_genomic.fna/target_genomes.txt --output GCF_020866905.1_ASM2086690v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:15:27,962] [INFO] Task succeeded: fastANI
[2024-01-25 20:15:27,962] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg59c3a267-5b93-4f61-b7a1-5a7fdf6a259c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:15:27,962] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg59c3a267-5b93-4f61-b7a1-5a7fdf6a259c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:15:27,970] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:15:27,970] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:15:27,971] [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
Salinimicrobium terrae	strain=DSM 17865	GCA_000424665.1	470866	470866	type	True	81.3693	702	1189	95	below_threshold
Salinimicrobium xinjiangense	strain=DSM 19287	GCA_000423585.1	438596	438596	type	True	79.9914	561	1189	95	below_threshold
Salinimicrobium sediminis	strain=CGMCC 1.12641	GCA_900215295.1	1343891	1343891	type	True	79.8273	551	1189	95	below_threshold
Salinimicrobium oceani	strain=J15B91	GCA_012037645.1	2722702	2722702	type	True	79.7627	512	1189	95	below_threshold
Salinimicrobium catena	strain=CGMCC 1.6101	GCA_900102915.1	390640	390640	type	True	78.5287	311	1189	95	below_threshold
Salinimicrobium marinum	strain=KCTC 12719	GCA_014651535.1	680283	680283	type	True	78.1023	270	1189	95	below_threshold
Gramella aestuarii	strain=BS12	GCA_009735585.1	1028746	1028746	type	True	77.3127	124	1189	95	below_threshold
Salegentibacter lacus	strain=LM13S	GCA_020164555.1	2873599	2873599	type	True	77.167	150	1189	95	below_threshold
Gramella echinicola	strain=DSM 19838	GCA_000423065.1	279359	279359	type	True	76.8641	124	1189	95	below_threshold
Gramella salexigens	strain=LPB0144	GCA_001889005.1	1913577	1913577	type	True	76.8556	105	1189	95	below_threshold
Zunongwangia mangrovi	strain=DSM 24499	GCA_900112105.1	1334022	1334022	type	True	76.8527	106	1189	95	below_threshold
Aequorivita lipolytica	strain=Y10-2	GCA_007997135.1	153267	153267	type	True	76.073	53	1189	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:15:27,973] [INFO] DFAST Taxonomy check result was written to GCF_020866905.1_ASM2086690v1_genomic.fna/tc_result.tsv
[2024-01-25 20:15:27,974] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:15:27,974] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:15:27,974] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg59c3a267-5b93-4f61-b7a1-5a7fdf6a259c/dqc_reference/checkm_data
[2024-01-25 20:15:27,975] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:15:28,025] [INFO] Task started: CheckM
[2024-01-25 20:15:28,025] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020866905.1_ASM2086690v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020866905.1_ASM2086690v1_genomic.fna/checkm_input GCF_020866905.1_ASM2086690v1_genomic.fna/checkm_result
[2024-01-25 20:16:06,608] [INFO] Task succeeded: CheckM
[2024-01-25 20:16:06,609] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:16:06,629] [INFO] ===== Completeness check finished =====
[2024-01-25 20:16:06,629] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:16:06,630] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020866905.1_ASM2086690v1_genomic.fna/markers.fasta)
[2024-01-25 20:16:06,630] [INFO] Task started: Blastn
[2024-01-25 20:16:06,630] [INFO] Running command: blastn -query GCF_020866905.1_ASM2086690v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg59c3a267-5b93-4f61-b7a1-5a7fdf6a259c/dqc_reference/reference_markers_gtdb.fasta -out GCF_020866905.1_ASM2086690v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:16:07,509] [INFO] Task succeeded: Blastn
[2024-01-25 20:16:07,512] [INFO] Selected 11 target genomes.
[2024-01-25 20:16:07,512] [INFO] Target genome list was writen to GCF_020866905.1_ASM2086690v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:16:07,517] [INFO] Task started: fastANI
[2024-01-25 20:16:07,518] [INFO] Running command: fastANI --query /var/lib/cwl/stgf46ad1d9-747a-4b46-b01a-0b2849a224aa/GCF_020866905.1_ASM2086690v1_genomic.fna.gz --refList GCF_020866905.1_ASM2086690v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020866905.1_ASM2086690v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:16:14,990] [INFO] Task succeeded: fastANI
[2024-01-25 20:16:14,997] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:16:14,997] [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_000424665.1	s__Salinimicrobium terrae	81.3693	702	1189	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423585.1	s__Salinimicrobium xinjiangense	79.999	561	1189	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012038135.1	s__Salinimicrobium sp012038135	79.9433	576	1189	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215295.1	s__Salinimicrobium sediminis	79.8273	551	1189	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102915.1	s__Salinimicrobium catena	78.5287	311	1189	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salinimicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014651535.1	s__Salinimicrobium marinum	78.0757	272	1189	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009735585.1	s__Gramella aestuarii	77.3447	124	1189	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745315.1	s__Salegentibacter sp000745315	77.2136	162	1189	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002078605.1	s__Salegentibacter sediminis	77.1332	144	1189	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001889005.1	s__Gramella salexigens	76.8556	105	1189	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423065.1	s__Gramella echinicola	76.8457	125	1189	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	97.44	97.44	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:16:15,000] [INFO] GTDB search result was written to GCF_020866905.1_ASM2086690v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:16:15,001] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:16:15,003] [INFO] DFAST_QC result json was written to GCF_020866905.1_ASM2086690v1_genomic.fna/dqc_result.json
[2024-01-25 20:16:15,003] [INFO] DFAST_QC completed!
[2024-01-25 20:16:15,003] [INFO] Total running time: 0h1m10s