[2024-01-24 13:10:18,732] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:10:18,740] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:10:18,740] [INFO] DQC Reference Directory: /var/lib/cwl/stg756e5e7f-2f3d-47e0-8c41-3db1af72cb8a/dqc_reference
[2024-01-24 13:10:19,995] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:10:19,997] [INFO] Task started: Prodigal
[2024-01-24 13:10:19,997] [INFO] Running command: gunzip -c /var/lib/cwl/stgd21d18d4-2776-4d32-a3bd-f586e2acd71c/GCF_014384905.1_ASM1438490v1_genomic.fna.gz | prodigal -d GCF_014384905.1_ASM1438490v1_genomic.fna/cds.fna -a GCF_014384905.1_ASM1438490v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:27,791] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:27,791] [INFO] Task started: HMMsearch
[2024-01-24 13:10:27,791] [INFO] Running command: hmmsearch --tblout GCF_014384905.1_ASM1438490v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg756e5e7f-2f3d-47e0-8c41-3db1af72cb8a/dqc_reference/reference_markers.hmm GCF_014384905.1_ASM1438490v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:28,114] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:28,115] [INFO] Found 6/6 markers.
[2024-01-24 13:10:28,149] [INFO] Query marker FASTA was written to GCF_014384905.1_ASM1438490v1_genomic.fna/markers.fasta
[2024-01-24 13:10:28,149] [INFO] Task started: Blastn
[2024-01-24 13:10:28,150] [INFO] Running command: blastn -query GCF_014384905.1_ASM1438490v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg756e5e7f-2f3d-47e0-8c41-3db1af72cb8a/dqc_reference/reference_markers.fasta -out GCF_014384905.1_ASM1438490v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:28,806] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:28,809] [INFO] Selected 24 target genomes.
[2024-01-24 13:10:28,810] [INFO] Target genome list was writen to GCF_014384905.1_ASM1438490v1_genomic.fna/target_genomes.txt
[2024-01-24 13:10:28,818] [INFO] Task started: fastANI
[2024-01-24 13:10:28,818] [INFO] Running command: fastANI --query /var/lib/cwl/stgd21d18d4-2776-4d32-a3bd-f586e2acd71c/GCF_014384905.1_ASM1438490v1_genomic.fna.gz --refList GCF_014384905.1_ASM1438490v1_genomic.fna/target_genomes.txt --output GCF_014384905.1_ASM1438490v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:44,093] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:44,094] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg756e5e7f-2f3d-47e0-8c41-3db1af72cb8a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:44,095] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg756e5e7f-2f3d-47e0-8c41-3db1af72cb8a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:44,100] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:10:44,101] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:44,101] [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
Fumia xinanensis	strain=NSJ-33	GCA_014384905.1	2763659	2763659	type	True	100.0	937	938	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:10:44,103] [INFO] DFAST Taxonomy check result was written to GCF_014384905.1_ASM1438490v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:44,104] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:44,104] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:44,104] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg756e5e7f-2f3d-47e0-8c41-3db1af72cb8a/dqc_reference/checkm_data
[2024-01-24 13:10:44,106] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:44,135] [INFO] Task started: CheckM
[2024-01-24 13:10:44,135] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014384905.1_ASM1438490v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014384905.1_ASM1438490v1_genomic.fna/checkm_input GCF_014384905.1_ASM1438490v1_genomic.fna/checkm_result
[2024-01-24 13:11:12,725] [INFO] Task succeeded: CheckM
[2024-01-24 13:11:12,726] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:11:12,766] [INFO] ===== Completeness check finished =====
[2024-01-24 13:11:12,766] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:11:12,767] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014384905.1_ASM1438490v1_genomic.fna/markers.fasta)
[2024-01-24 13:11:12,767] [INFO] Task started: Blastn
[2024-01-24 13:11:12,767] [INFO] Running command: blastn -query GCF_014384905.1_ASM1438490v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg756e5e7f-2f3d-47e0-8c41-3db1af72cb8a/dqc_reference/reference_markers_gtdb.fasta -out GCF_014384905.1_ASM1438490v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:11:13,847] [INFO] Task succeeded: Blastn
[2024-01-24 13:11:13,852] [INFO] Selected 21 target genomes.
[2024-01-24 13:11:13,853] [INFO] Target genome list was writen to GCF_014384905.1_ASM1438490v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:11:13,907] [INFO] Task started: fastANI
[2024-01-24 13:11:13,907] [INFO] Running command: fastANI --query /var/lib/cwl/stgd21d18d4-2776-4d32-a3bd-f586e2acd71c/GCF_014384905.1_ASM1438490v1_genomic.fna.gz --refList GCF_014384905.1_ASM1438490v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014384905.1_ASM1438490v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:21,951] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:21,962] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:11:21,963] [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_014384905.1	s__QANG01 sp003150145	100.0	937	938	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__QANG01	95.0	98.90	98.90	0.88	0.88	2	conclusive
GCA_904396495.1	s__QANG01 sp904396495	81.8426	526	938	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__QANG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018713335.1	s__Merdivicinus intestinigallinarum	77.0795	118	938	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Merdivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018716725.1	s__Merdivicinus excrementipullorum	76.9505	120	938	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Merdivicinus	95.0	99.35	99.04	0.91	0.87	4	-
GCA_905214265.1	s__Merdivicinus sp905214265	76.8717	82	938	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Merdivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018716285.1	s__Merdivicinus faecavium	76.6023	98	938	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Merdivicinus	95.0	99.37	98.77	0.95	0.93	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:11:21,966] [INFO] GTDB search result was written to GCF_014384905.1_ASM1438490v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:21,967] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:21,970] [INFO] DFAST_QC result json was written to GCF_014384905.1_ASM1438490v1_genomic.fna/dqc_result.json
[2024-01-24 13:11:21,970] [INFO] DFAST_QC completed!
[2024-01-24 13:11:21,970] [INFO] Total running time: 0h1m3s