[2024-01-25 19:09:50,674] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:09:50,675] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:09:50,676] [INFO] DQC Reference Directory: /var/lib/cwl/stgb756c43d-6cc9-401a-8ef5-ef41d49634a9/dqc_reference
[2024-01-25 19:09:51,842] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:09:51,842] [INFO] Task started: Prodigal
[2024-01-25 19:09:51,843] [INFO] Running command: gunzip -c /var/lib/cwl/stgaef451c1-5fa6-4267-a93a-6b5a77185f1e/GCF_025567095.1_ASM2556709v1_genomic.fna.gz | prodigal -d GCF_025567095.1_ASM2556709v1_genomic.fna/cds.fna -a GCF_025567095.1_ASM2556709v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:09:59,880] [INFO] Task succeeded: Prodigal
[2024-01-25 19:09:59,881] [INFO] Task started: HMMsearch
[2024-01-25 19:09:59,881] [INFO] Running command: hmmsearch --tblout GCF_025567095.1_ASM2556709v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb756c43d-6cc9-401a-8ef5-ef41d49634a9/dqc_reference/reference_markers.hmm GCF_025567095.1_ASM2556709v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:10:00,145] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:10:00,146] [INFO] Found 6/6 markers.
[2024-01-25 19:10:00,179] [INFO] Query marker FASTA was written to GCF_025567095.1_ASM2556709v1_genomic.fna/markers.fasta
[2024-01-25 19:10:00,180] [INFO] Task started: Blastn
[2024-01-25 19:10:00,180] [INFO] Running command: blastn -query GCF_025567095.1_ASM2556709v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb756c43d-6cc9-401a-8ef5-ef41d49634a9/dqc_reference/reference_markers.fasta -out GCF_025567095.1_ASM2556709v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:10:00,778] [INFO] Task succeeded: Blastn
[2024-01-25 19:10:00,782] [INFO] Selected 32 target genomes.
[2024-01-25 19:10:00,782] [INFO] Target genome list was writen to GCF_025567095.1_ASM2556709v1_genomic.fna/target_genomes.txt
[2024-01-25 19:10:00,800] [INFO] Task started: fastANI
[2024-01-25 19:10:00,801] [INFO] Running command: fastANI --query /var/lib/cwl/stgaef451c1-5fa6-4267-a93a-6b5a77185f1e/GCF_025567095.1_ASM2556709v1_genomic.fna.gz --refList GCF_025567095.1_ASM2556709v1_genomic.fna/target_genomes.txt --output GCF_025567095.1_ASM2556709v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:10:17,049] [INFO] Task succeeded: fastANI
[2024-01-25 19:10:17,049] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb756c43d-6cc9-401a-8ef5-ef41d49634a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:10:17,049] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb756c43d-6cc9-401a-8ef5-ef41d49634a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:10:17,056] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:10:17,056] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:10:17,056] [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
Mediterraneibacter butyricigenes	strain=KCTC 15684	GCA_003574295.1	2316025	2316025	type	True	85.2858	81	1234	95	below_threshold
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	82.0542	70	1234	95	below_threshold
Anaerobutyricum hallii	strain=DSM 3353	GCA_000173975.1	39488	39488	type	True	80.1503	54	1234	95	below_threshold
Jutongia huaianensis	strain=NSJ-37	GCA_014384985.1	2763668	2763668	type	True	79.7249	53	1234	95	below_threshold
Roseburia faecis	strain=M72	GCA_001406815.1	301302	301302	type	True	79.5756	72	1234	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_000155205.1	46228	46228	type	True	79.3334	55	1234	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	79.3108	55	1234	95	below_threshold
Jingyaoa shaoxingensis	strain=NSJ-46	GCA_014385005.1	2763671	2763671	type	True	79.0956	67	1234	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:10:17,058] [INFO] DFAST Taxonomy check result was written to GCF_025567095.1_ASM2556709v1_genomic.fna/tc_result.tsv
[2024-01-25 19:10:17,058] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:10:17,058] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:10:17,059] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb756c43d-6cc9-401a-8ef5-ef41d49634a9/dqc_reference/checkm_data
[2024-01-25 19:10:17,059] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:10:17,099] [INFO] Task started: CheckM
[2024-01-25 19:10:17,099] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025567095.1_ASM2556709v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025567095.1_ASM2556709v1_genomic.fna/checkm_input GCF_025567095.1_ASM2556709v1_genomic.fna/checkm_result
[2024-01-25 19:10:45,079] [INFO] Task succeeded: CheckM
[2024-01-25 19:10:45,080] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:10:45,101] [INFO] ===== Completeness check finished =====
[2024-01-25 19:10:45,101] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:10:45,101] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025567095.1_ASM2556709v1_genomic.fna/markers.fasta)
[2024-01-25 19:10:45,102] [INFO] Task started: Blastn
[2024-01-25 19:10:45,102] [INFO] Running command: blastn -query GCF_025567095.1_ASM2556709v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb756c43d-6cc9-401a-8ef5-ef41d49634a9/dqc_reference/reference_markers_gtdb.fasta -out GCF_025567095.1_ASM2556709v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:10:46,088] [INFO] Task succeeded: Blastn
[2024-01-25 19:10:46,093] [INFO] Selected 28 target genomes.
[2024-01-25 19:10:46,093] [INFO] Target genome list was writen to GCF_025567095.1_ASM2556709v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:10:46,115] [INFO] Task started: fastANI
[2024-01-25 19:10:46,116] [INFO] Running command: fastANI --query /var/lib/cwl/stgaef451c1-5fa6-4267-a93a-6b5a77185f1e/GCF_025567095.1_ASM2556709v1_genomic.fna.gz --refList GCF_025567095.1_ASM2556709v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025567095.1_ASM2556709v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:10:59,960] [INFO] Task succeeded: fastANI
[2024-01-25 19:10:59,964] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:10:59,965] [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
GCA_003478935.1	s__KLE1615 sp900066985	96.3981	1015	1234	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__KLE1615	95.0	97.20	95.19	0.86	0.78	12	conclusive
GCF_003470905.1	s__Roseburia sp003470905	79.7458	74	1234	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	98.69	98.30	0.90	0.82	7	-
GCF_009696065.1	s__Oliverpabstia intestinalis	77.1023	53	1234	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oliverpabstia	95.0	97.25	96.88	0.81	0.78	19	-
GCA_905214365.1	s__KLE1615 sp905214365	77.0601	107	1234	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__KLE1615	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:10:59,966] [INFO] GTDB search result was written to GCF_025567095.1_ASM2556709v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:10:59,966] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:10:59,969] [INFO] DFAST_QC result json was written to GCF_025567095.1_ASM2556709v1_genomic.fna/dqc_result.json
[2024-01-25 19:10:59,970] [INFO] DFAST_QC completed!
[2024-01-25 19:10:59,970] [INFO] Total running time: 0h1m9s