[2024-01-24 11:05:24,601] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:24,604] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:24,604] [INFO] DQC Reference Directory: /var/lib/cwl/stg90a4fe10-f9ea-42ff-9614-f9301608ce96/dqc_reference
[2024-01-24 11:05:25,864] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:25,864] [INFO] Task started: Prodigal
[2024-01-24 11:05:25,865] [INFO] Running command: gunzip -c /var/lib/cwl/stg39d4bd58-b250-4c3e-96fc-a42c4b9981dc/GCF_014518315.1_ASM1451831v1_genomic.fna.gz | prodigal -d GCF_014518315.1_ASM1451831v1_genomic.fna/cds.fna -a GCF_014518315.1_ASM1451831v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:45,255] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:45,255] [INFO] Task started: HMMsearch
[2024-01-24 11:05:45,255] [INFO] Running command: hmmsearch --tblout GCF_014518315.1_ASM1451831v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg90a4fe10-f9ea-42ff-9614-f9301608ce96/dqc_reference/reference_markers.hmm GCF_014518315.1_ASM1451831v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:45,565] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:45,566] [INFO] Found 6/6 markers.
[2024-01-24 11:05:45,598] [INFO] Query marker FASTA was written to GCF_014518315.1_ASM1451831v1_genomic.fna/markers.fasta
[2024-01-24 11:05:45,598] [INFO] Task started: Blastn
[2024-01-24 11:05:45,598] [INFO] Running command: blastn -query GCF_014518315.1_ASM1451831v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg90a4fe10-f9ea-42ff-9614-f9301608ce96/dqc_reference/reference_markers.fasta -out GCF_014518315.1_ASM1451831v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:46,219] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:46,223] [INFO] Selected 24 target genomes.
[2024-01-24 11:05:46,223] [INFO] Target genome list was writen to GCF_014518315.1_ASM1451831v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:46,233] [INFO] Task started: fastANI
[2024-01-24 11:05:46,233] [INFO] Running command: fastANI --query /var/lib/cwl/stg39d4bd58-b250-4c3e-96fc-a42c4b9981dc/GCF_014518315.1_ASM1451831v1_genomic.fna.gz --refList GCF_014518315.1_ASM1451831v1_genomic.fna/target_genomes.txt --output GCF_014518315.1_ASM1451831v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:02,586] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:02,587] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg90a4fe10-f9ea-42ff-9614-f9301608ce96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:02,587] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg90a4fe10-f9ea-42ff-9614-f9301608ce96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:02,592] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:06:02,593] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:06:02,593] [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
Taishania pollutisoli	strain=CZZ-1	GCA_014518315.1	2766479	2766479	type	True	100.0	1228	1231	95	conclusive
Fluviicola taffensis	strain=DSM 16823	GCA_000194605.1	191579	191579	type	True	76.993	69	1231	95	below_threshold
Fluviicola chungangensis	strain=MAH-3	GCA_007558725.1	2597671	2597671	type	True	76.8821	82	1231	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:02,594] [INFO] DFAST Taxonomy check result was written to GCF_014518315.1_ASM1451831v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:02,595] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:02,595] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:02,596] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg90a4fe10-f9ea-42ff-9614-f9301608ce96/dqc_reference/checkm_data
[2024-01-24 11:06:02,597] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:02,676] [INFO] Task started: CheckM
[2024-01-24 11:06:02,676] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014518315.1_ASM1451831v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014518315.1_ASM1451831v1_genomic.fna/checkm_input GCF_014518315.1_ASM1451831v1_genomic.fna/checkm_result
[2024-01-24 11:07:00,345] [INFO] Task succeeded: CheckM
[2024-01-24 11:07:00,347] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:07:00,369] [INFO] ===== Completeness check finished =====
[2024-01-24 11:07:00,369] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:07:00,370] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014518315.1_ASM1451831v1_genomic.fna/markers.fasta)
[2024-01-24 11:07:00,370] [INFO] Task started: Blastn
[2024-01-24 11:07:00,370] [INFO] Running command: blastn -query GCF_014518315.1_ASM1451831v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg90a4fe10-f9ea-42ff-9614-f9301608ce96/dqc_reference/reference_markers_gtdb.fasta -out GCF_014518315.1_ASM1451831v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:07:01,173] [INFO] Task succeeded: Blastn
[2024-01-24 11:07:01,177] [INFO] Selected 22 target genomes.
[2024-01-24 11:07:01,177] [INFO] Target genome list was writen to GCF_014518315.1_ASM1451831v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:07:01,216] [INFO] Task started: fastANI
[2024-01-24 11:07:01,217] [INFO] Running command: fastANI --query /var/lib/cwl/stg39d4bd58-b250-4c3e-96fc-a42c4b9981dc/GCF_014518315.1_ASM1451831v1_genomic.fna.gz --refList GCF_014518315.1_ASM1451831v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014518315.1_ASM1451831v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:07:14,152] [INFO] Task succeeded: fastANI
[2024-01-24 11:07:14,164] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:07:14,165] [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_014518315.1	s__Taishania pollutisoli	100.0	1228	1231	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Taishania	95.0	99.31	99.31	0.93	0.93	2	conclusive
GCA_002409405.1	s__Taishania sp002409405	86.0047	960	1231	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Taishania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017984635.1	s__M0103 sp017984635	77.4421	54	1231	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__M0103	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903945495.1	s__M0103 sp903945495	77.32	58	1231	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__M0103	95.0	99.87	99.80	0.95	0.92	6	-
GCF_007558725.1	s__Fluviicola chungangensis	76.9062	81	1231	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Fluviicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003856375.1	s__Fluviicola amylolytica	76.878	95	1231	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Fluviicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:07:14,167] [INFO] GTDB search result was written to GCF_014518315.1_ASM1451831v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:07:14,167] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:07:14,169] [INFO] DFAST_QC result json was written to GCF_014518315.1_ASM1451831v1_genomic.fna/dqc_result.json
[2024-01-24 11:07:14,170] [INFO] DFAST_QC completed!
[2024-01-24 11:07:14,170] [INFO] Total running time: 0h1m50s