[2024-01-24 15:02:23,963] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:23,965] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:23,965] [INFO] DQC Reference Directory: /var/lib/cwl/stga5b5c17f-1401-47d1-b5f1-6cc6e031f23c/dqc_reference
[2024-01-24 15:02:26,429] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:26,430] [INFO] Task started: Prodigal
[2024-01-24 15:02:26,431] [INFO] Running command: gunzip -c /var/lib/cwl/stg8b7c8105-8363-4621-bdaa-1cb2eb3ead18/GCF_900660705.1_57612_F01-3_genomic.fna.gz | prodigal -d GCF_900660705.1_57612_F01-3_genomic.fna/cds.fna -a GCF_900660705.1_57612_F01-3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:28,196] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:28,196] [INFO] Task started: HMMsearch
[2024-01-24 15:02:28,197] [INFO] Running command: hmmsearch --tblout GCF_900660705.1_57612_F01-3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga5b5c17f-1401-47d1-b5f1-6cc6e031f23c/dqc_reference/reference_markers.hmm GCF_900660705.1_57612_F01-3_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:28,512] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:28,513] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg8b7c8105-8363-4621-bdaa-1cb2eb3ead18/GCF_900660705.1_57612_F01-3_genomic.fna.gz]
[2024-01-24 15:02:28,527] [INFO] Query marker FASTA was written to GCF_900660705.1_57612_F01-3_genomic.fna/markers.fasta
[2024-01-24 15:02:28,529] [INFO] Task started: Blastn
[2024-01-24 15:02:28,529] [INFO] Running command: blastn -query GCF_900660705.1_57612_F01-3_genomic.fna/markers.fasta -db /var/lib/cwl/stga5b5c17f-1401-47d1-b5f1-6cc6e031f23c/dqc_reference/reference_markers.fasta -out GCF_900660705.1_57612_F01-3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:32,734] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:32,737] [INFO] Selected 7 target genomes.
[2024-01-24 15:02:32,737] [INFO] Target genome list was writen to GCF_900660705.1_57612_F01-3_genomic.fna/target_genomes.txt
[2024-01-24 15:02:32,764] [INFO] Task started: fastANI
[2024-01-24 15:02:32,764] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b7c8105-8363-4621-bdaa-1cb2eb3ead18/GCF_900660705.1_57612_F01-3_genomic.fna.gz --refList GCF_900660705.1_57612_F01-3_genomic.fna/target_genomes.txt --output GCF_900660705.1_57612_F01-3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:02:34,175] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:34,175] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga5b5c17f-1401-47d1-b5f1-6cc6e031f23c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:02:34,176] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga5b5c17f-1401-47d1-b5f1-6cc6e031f23c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:02:34,181] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:02:34,181] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:02:34,182] [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
Mycoplasmopsis columbinasalis	strain=NCTC10184	GCA_900660705.1	114880	114880	type	True	100.0	283	283	95	conclusive
Mycoplasmopsis columbina	strain=NCTC10178	GCA_900660685.1	114881	114881	type	True	78.3596	51	283	95	below_threshold
Mycoplasmopsis columbina	strain=ATCC 29257	GCA_000712175.1	114881	114881	type	True	78.1176	50	283	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:02:34,183] [INFO] DFAST Taxonomy check result was written to GCF_900660705.1_57612_F01-3_genomic.fna/tc_result.tsv
[2024-01-24 15:02:34,183] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:02:34,184] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:02:34,184] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga5b5c17f-1401-47d1-b5f1-6cc6e031f23c/dqc_reference/checkm_data
[2024-01-24 15:02:34,185] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:02:34,196] [INFO] Task started: CheckM
[2024-01-24 15:02:34,197] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900660705.1_57612_F01-3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900660705.1_57612_F01-3_genomic.fna/checkm_input GCF_900660705.1_57612_F01-3_genomic.fna/checkm_result
[2024-01-24 15:02:55,269] [INFO] Task succeeded: CheckM
[2024-01-24 15:02:55,270] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:02:55,289] [INFO] ===== Completeness check finished =====
[2024-01-24 15:02:55,289] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:02:55,290] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900660705.1_57612_F01-3_genomic.fna/markers.fasta)
[2024-01-24 15:02:55,290] [INFO] Task started: Blastn
[2024-01-24 15:02:55,291] [INFO] Running command: blastn -query GCF_900660705.1_57612_F01-3_genomic.fna/markers.fasta -db /var/lib/cwl/stga5b5c17f-1401-47d1-b5f1-6cc6e031f23c/dqc_reference/reference_markers_gtdb.fasta -out GCF_900660705.1_57612_F01-3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:56,104] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:56,108] [INFO] Selected 17 target genomes.
[2024-01-24 15:02:56,109] [INFO] Target genome list was writen to GCF_900660705.1_57612_F01-3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:02:56,154] [INFO] Task started: fastANI
[2024-01-24 15:02:56,155] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b7c8105-8363-4621-bdaa-1cb2eb3ead18/GCF_900660705.1_57612_F01-3_genomic.fna.gz --refList GCF_900660705.1_57612_F01-3_genomic.fna/target_genomes_gtdb.txt --output GCF_900660705.1_57612_F01-3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:03:02,565] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:02,571] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:03:02,571] [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_900660705.1	s__Mycoplasmopsis columbinasalis	100.0	283	283	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900660685.1	s__Mycoplasmopsis columbina	78.3596	51	283	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis	95.0	99.36	98.73	0.99	0.99	3	-
--------------------------------------------------------------------------------
[2024-01-24 15:03:02,573] [INFO] GTDB search result was written to GCF_900660705.1_57612_F01-3_genomic.fna/result_gtdb.tsv
[2024-01-24 15:03:02,574] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:03:02,578] [INFO] DFAST_QC result json was written to GCF_900660705.1_57612_F01-3_genomic.fna/dqc_result.json
[2024-01-24 15:03:02,578] [INFO] DFAST_QC completed!
[2024-01-24 15:03:02,579] [INFO] Total running time: 0h0m39s