[2024-01-25 17:44:05,667] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:44:05,669] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:44:05,669] [INFO] DQC Reference Directory: /var/lib/cwl/stgf7853fdd-93c6-4c27-8627-c8dbd8142711/dqc_reference
[2024-01-25 17:44:06,871] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:44:06,871] [INFO] Task started: Prodigal
[2024-01-25 17:44:06,872] [INFO] Running command: gunzip -c /var/lib/cwl/stg7ade53d0-a15d-48ae-8a9b-fd240a1d5fd1/GCF_012934885.1_ASM1293488v1_genomic.fna.gz | prodigal -d GCF_012934885.1_ASM1293488v1_genomic.fna/cds.fna -a GCF_012934885.1_ASM1293488v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:44:08,089] [INFO] Task succeeded: Prodigal
[2024-01-25 17:44:08,090] [INFO] Task started: HMMsearch
[2024-01-25 17:44:08,090] [INFO] Running command: hmmsearch --tblout GCF_012934885.1_ASM1293488v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf7853fdd-93c6-4c27-8627-c8dbd8142711/dqc_reference/reference_markers.hmm GCF_012934885.1_ASM1293488v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:44:08,241] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:44:08,242] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7ade53d0-a15d-48ae-8a9b-fd240a1d5fd1/GCF_012934885.1_ASM1293488v1_genomic.fna.gz]
[2024-01-25 17:44:08,254] [INFO] Query marker FASTA was written to GCF_012934885.1_ASM1293488v1_genomic.fna/markers.fasta
[2024-01-25 17:44:08,254] [INFO] Task started: Blastn
[2024-01-25 17:44:08,254] [INFO] Running command: blastn -query GCF_012934885.1_ASM1293488v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7853fdd-93c6-4c27-8627-c8dbd8142711/dqc_reference/reference_markers.fasta -out GCF_012934885.1_ASM1293488v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:44:08,770] [INFO] Task succeeded: Blastn
[2024-01-25 17:44:08,773] [INFO] Selected 10 target genomes.
[2024-01-25 17:44:08,773] [INFO] Target genome list was writen to GCF_012934885.1_ASM1293488v1_genomic.fna/target_genomes.txt
[2024-01-25 17:44:08,780] [INFO] Task started: fastANI
[2024-01-25 17:44:08,780] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ade53d0-a15d-48ae-8a9b-fd240a1d5fd1/GCF_012934885.1_ASM1293488v1_genomic.fna.gz --refList GCF_012934885.1_ASM1293488v1_genomic.fna/target_genomes.txt --output GCF_012934885.1_ASM1293488v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:44:10,829] [INFO] Task succeeded: fastANI
[2024-01-25 17:44:10,830] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf7853fdd-93c6-4c27-8627-c8dbd8142711/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:44:10,830] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf7853fdd-93c6-4c27-8627-c8dbd8142711/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:44:10,835] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:44:10,835] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:44:10,835] [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
Mycoplasma struthionis	strain=237IA	GCA_003855455.1	538220	538220	type	True	79.1415	57	258	95	below_threshold
Metamycoplasma anseris	strain=ATCC 49234	GCA_003285045.1	92400	92400	type	True	78.6072	51	258	95	below_threshold
Metamycoplasma anseris	strain=ATCC 49234	GCA_000702805.1	92400	92400	type	True	78.3486	53	258	95	below_threshold
Metamycoplasma falconis	strain=ATCC 51372	GCA_006385795.1	92403	92403	type	True	77.7212	54	258	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:44:10,839] [INFO] DFAST Taxonomy check result was written to GCF_012934885.1_ASM1293488v1_genomic.fna/tc_result.tsv
[2024-01-25 17:44:10,839] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:44:10,839] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:44:10,840] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf7853fdd-93c6-4c27-8627-c8dbd8142711/dqc_reference/checkm_data
[2024-01-25 17:44:10,840] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:44:10,851] [INFO] Task started: CheckM
[2024-01-25 17:44:10,851] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012934885.1_ASM1293488v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012934885.1_ASM1293488v1_genomic.fna/checkm_input GCF_012934885.1_ASM1293488v1_genomic.fna/checkm_result
[2024-01-25 17:44:21,675] [INFO] Task succeeded: CheckM
[2024-01-25 17:44:21,676] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:44:21,715] [INFO] ===== Completeness check finished =====
[2024-01-25 17:44:21,715] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:44:21,716] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012934885.1_ASM1293488v1_genomic.fna/markers.fasta)
[2024-01-25 17:44:21,716] [INFO] Task started: Blastn
[2024-01-25 17:44:21,716] [INFO] Running command: blastn -query GCF_012934885.1_ASM1293488v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7853fdd-93c6-4c27-8627-c8dbd8142711/dqc_reference/reference_markers_gtdb.fasta -out GCF_012934885.1_ASM1293488v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:44:22,482] [INFO] Task succeeded: Blastn
[2024-01-25 17:44:22,485] [INFO] Selected 17 target genomes.
[2024-01-25 17:44:22,485] [INFO] Target genome list was writen to GCF_012934885.1_ASM1293488v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:44:22,499] [INFO] Task started: fastANI
[2024-01-25 17:44:22,499] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ade53d0-a15d-48ae-8a9b-fd240a1d5fd1/GCF_012934885.1_ASM1293488v1_genomic.fna.gz --refList GCF_012934885.1_ASM1293488v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012934885.1_ASM1293488v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:44:28,760] [INFO] Task succeeded: fastANI
[2024-01-25 17:44:28,765] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:44:28,765] [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_012934885.1	s__Metamycoplasma sp012934885	100.0	258	258	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	98.25	98.25	0.95	0.95	2	conclusive
GCF_003332325.1	s__Metamycoplasma phocidae	82.3193	188	258	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003855455.1	s__Metamycoplasma struthionis	79.1891	57	258	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	98.82	98.82	0.96	0.96	2	-
GCF_000367765.1	s__Metamycoplasma auris_A	78.887	50	258	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000702805.1	s__Metamycoplasma anseris	78.4253	52	258	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006385795.1	s__Metamycoplasma falconis	77.7212	54	258	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:44:28,767] [INFO] GTDB search result was written to GCF_012934885.1_ASM1293488v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:44:28,767] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:44:28,770] [INFO] DFAST_QC result json was written to GCF_012934885.1_ASM1293488v1_genomic.fna/dqc_result.json
[2024-01-25 17:44:28,770] [INFO] DFAST_QC completed!
[2024-01-25 17:44:28,770] [INFO] Total running time: 0h0m23s