[2024-01-24 12:47:22,151] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:22,153] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:22,153] [INFO] DQC Reference Directory: /var/lib/cwl/stg844de882-98ad-4c5b-a512-bacbc17f29f5/dqc_reference
[2024-01-24 12:47:23,396] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:23,397] [INFO] Task started: Prodigal
[2024-01-24 12:47:23,397] [INFO] Running command: gunzip -c /var/lib/cwl/stg167e4de9-57a6-40bc-89d7-4e06e36ddea1/GCF_014384765.1_ASM1438476v1_genomic.fna.gz | prodigal -d GCF_014384765.1_ASM1438476v1_genomic.fna/cds.fna -a GCF_014384765.1_ASM1438476v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:30,344] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:30,345] [INFO] Task started: HMMsearch
[2024-01-24 12:47:30,345] [INFO] Running command: hmmsearch --tblout GCF_014384765.1_ASM1438476v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg844de882-98ad-4c5b-a512-bacbc17f29f5/dqc_reference/reference_markers.hmm GCF_014384765.1_ASM1438476v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:30,604] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:30,605] [INFO] Found 6/6 markers.
[2024-01-24 12:47:30,636] [INFO] Query marker FASTA was written to GCF_014384765.1_ASM1438476v1_genomic.fna/markers.fasta
[2024-01-24 12:47:30,637] [INFO] Task started: Blastn
[2024-01-24 12:47:30,637] [INFO] Running command: blastn -query GCF_014384765.1_ASM1438476v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg844de882-98ad-4c5b-a512-bacbc17f29f5/dqc_reference/reference_markers.fasta -out GCF_014384765.1_ASM1438476v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:31,370] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:31,374] [INFO] Selected 22 target genomes.
[2024-01-24 12:47:31,375] [INFO] Target genome list was writen to GCF_014384765.1_ASM1438476v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:31,386] [INFO] Task started: fastANI
[2024-01-24 12:47:31,387] [INFO] Running command: fastANI --query /var/lib/cwl/stg167e4de9-57a6-40bc-89d7-4e06e36ddea1/GCF_014384765.1_ASM1438476v1_genomic.fna.gz --refList GCF_014384765.1_ASM1438476v1_genomic.fna/target_genomes.txt --output GCF_014384765.1_ASM1438476v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:46,288] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:46,289] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg844de882-98ad-4c5b-a512-bacbc17f29f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:46,289] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg844de882-98ad-4c5b-a512-bacbc17f29f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:46,295] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:47:46,295] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:46,295] [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
Feifania hominis	strain=BX7	GCA_014384765.1	2763660	2763660	type	True	100.0	781	781	95	conclusive
Bittarella massiliensis	strain=GD6	GCA_001486165.1	1720313	1720313	type	True	77.3456	75	781	95	below_threshold
Anaerotruncus massiliensis	strain=AT3	GCA_900199635.1	1673720	1673720	type	True	77.2439	99	781	95	below_threshold
Ligaoa zhengdingensis	strain=NSJ-31	GCA_014384885.1	2763658	2763658	type	True	76.3908	63	781	95	below_threshold
Dactylosporangium sucinum	strain=JCM 19831	GCA_014647515.1	1424081	1424081	type	True	74.9554	50	781	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:46,297] [INFO] DFAST Taxonomy check result was written to GCF_014384765.1_ASM1438476v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:46,298] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:46,298] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:46,298] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg844de882-98ad-4c5b-a512-bacbc17f29f5/dqc_reference/checkm_data
[2024-01-24 12:47:46,299] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:46,335] [INFO] Task started: CheckM
[2024-01-24 12:47:46,336] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014384765.1_ASM1438476v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014384765.1_ASM1438476v1_genomic.fna/checkm_input GCF_014384765.1_ASM1438476v1_genomic.fna/checkm_result
[2024-01-24 12:48:13,926] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:13,927] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:13,947] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:13,948] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:13,948] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014384765.1_ASM1438476v1_genomic.fna/markers.fasta)
[2024-01-24 12:48:13,948] [INFO] Task started: Blastn
[2024-01-24 12:48:13,948] [INFO] Running command: blastn -query GCF_014384765.1_ASM1438476v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg844de882-98ad-4c5b-a512-bacbc17f29f5/dqc_reference/reference_markers_gtdb.fasta -out GCF_014384765.1_ASM1438476v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:15,341] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:15,346] [INFO] Selected 27 target genomes.
[2024-01-24 12:48:15,347] [INFO] Target genome list was writen to GCF_014384765.1_ASM1438476v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:15,367] [INFO] Task started: fastANI
[2024-01-24 12:48:15,367] [INFO] Running command: fastANI --query /var/lib/cwl/stg167e4de9-57a6-40bc-89d7-4e06e36ddea1/GCF_014384765.1_ASM1438476v1_genomic.fna.gz --refList GCF_014384765.1_ASM1438476v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014384765.1_ASM1438476v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:27,603] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:27,613] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:48:27,614] [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_014384765.1	s__BX7 sp014384765	100.0	781	781	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__BX7;g__BX7	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001486165.1	s__Bittarella massiliensis	77.3101	76	781	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Bittarella	95.0	97.23	96.02	0.88	0.84	8	-
GCA_004340125.1	s__Harryflintia acetispora	77.2658	78	781	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Harryflintia	95.0	98.73	98.54	0.92	0.90	6	-
GCF_900199635.1	s__Anaerotruncus massiliensis	77.195	101	781	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	98.56	98.01	0.95	0.93	6	-
GCA_014385095.1	s__Pararuminococcus sp014385095	76.811	58	781	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Pararuminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900552925.1	s__UBA1417 sp900552925	76.7112	53	781	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1417	95.0	98.06	97.73	0.91	0.83	5	-
GCF_018918025.1	s__ER4 sp900317525	76.6434	64	781	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	97.58	97.23	0.91	0.84	22	-
GCA_904420075.1	s__CAJFTX01 sp904420075	76.5275	70	781	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__BX7;g__CAJFTX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012719075.1	s__JAAYBB01 sp012719075	76.3678	67	781	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__BX7;g__JAAYBB01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:48:27,616] [INFO] GTDB search result was written to GCF_014384765.1_ASM1438476v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:27,616] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:27,620] [INFO] DFAST_QC result json was written to GCF_014384765.1_ASM1438476v1_genomic.fna/dqc_result.json
[2024-01-24 12:48:27,620] [INFO] DFAST_QC completed!
[2024-01-24 12:48:27,620] [INFO] Total running time: 0h1m5s