[2024-01-24 12:44:53,470] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:53,472] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:53,472] [INFO] DQC Reference Directory: /var/lib/cwl/stg521f3f55-08e8-4ebc-ae86-7db545dd55ab/dqc_reference
[2024-01-24 12:44:54,865] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:54,866] [INFO] Task started: Prodigal
[2024-01-24 12:44:54,866] [INFO] Running command: gunzip -c /var/lib/cwl/stg71815a7d-a5d5-4bf5-8be6-c2194339beac/GCF_003688445.1_ASM368844v1_genomic.fna.gz | prodigal -d GCF_003688445.1_ASM368844v1_genomic.fna/cds.fna -a GCF_003688445.1_ASM368844v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:55,921] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:55,921] [INFO] Task started: HMMsearch
[2024-01-24 12:44:55,921] [INFO] Running command: hmmsearch --tblout GCF_003688445.1_ASM368844v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg521f3f55-08e8-4ebc-ae86-7db545dd55ab/dqc_reference/reference_markers.hmm GCF_003688445.1_ASM368844v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:56,067] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:56,068] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg71815a7d-a5d5-4bf5-8be6-c2194339beac/GCF_003688445.1_ASM368844v1_genomic.fna.gz]
[2024-01-24 12:44:56,081] [INFO] Query marker FASTA was written to GCF_003688445.1_ASM368844v1_genomic.fna/markers.fasta
[2024-01-24 12:44:56,082] [INFO] Task started: Blastn
[2024-01-24 12:44:56,082] [INFO] Running command: blastn -query GCF_003688445.1_ASM368844v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg521f3f55-08e8-4ebc-ae86-7db545dd55ab/dqc_reference/reference_markers.fasta -out GCF_003688445.1_ASM368844v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:56,644] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:56,648] [INFO] Selected 13 target genomes.
[2024-01-24 12:44:56,649] [INFO] Target genome list was writen to GCF_003688445.1_ASM368844v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:56,684] [INFO] Task started: fastANI
[2024-01-24 12:44:56,684] [INFO] Running command: fastANI --query /var/lib/cwl/stg71815a7d-a5d5-4bf5-8be6-c2194339beac/GCF_003688445.1_ASM368844v1_genomic.fna.gz --refList GCF_003688445.1_ASM368844v1_genomic.fna/target_genomes.txt --output GCF_003688445.1_ASM368844v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:44:58,386] [INFO] Task succeeded: fastANI
[2024-01-24 12:44:58,386] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg521f3f55-08e8-4ebc-ae86-7db545dd55ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:44:58,386] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg521f3f55-08e8-4ebc-ae86-7db545dd55ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:44:58,393] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:44:58,393] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:44:58,393] [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
Metamycoplasma subdolum	strain=ATCC 29870	GCA_003688445.1	92407	92407	type	True	100.0	210	211	95	conclusive
Metamycoplasma anseris	strain=ATCC 49234	GCA_000702805.1	92400	92400	type	True	78.1399	56	211	95	below_threshold
Metamycoplasma anseris	strain=ATCC 49234	GCA_003285045.1	92400	92400	type	True	78.1053	58	211	95	below_threshold
Metamycoplasma cloacale	strain=ATCC 35276	GCA_000702745.1	92401	92401	type	True	78.0365	56	211	95	below_threshold
Metamycoplasma salivarium	strain=ATCC 23064	GCA_000485555.1	2124	2124	type	True	77.8347	56	211	95	below_threshold
Metamycoplasma salivarium	strain=NCTC10113	GCA_900660445.2	2124	2124	type	True	77.6698	60	211	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:44:58,395] [INFO] DFAST Taxonomy check result was written to GCF_003688445.1_ASM368844v1_genomic.fna/tc_result.tsv
[2024-01-24 12:44:58,396] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:44:58,396] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:44:58,396] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg521f3f55-08e8-4ebc-ae86-7db545dd55ab/dqc_reference/checkm_data
[2024-01-24 12:44:58,397] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:44:58,411] [INFO] Task started: CheckM
[2024-01-24 12:44:58,411] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003688445.1_ASM368844v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003688445.1_ASM368844v1_genomic.fna/checkm_input GCF_003688445.1_ASM368844v1_genomic.fna/checkm_result
[2024-01-24 12:45:10,741] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:10,743] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:10,764] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:10,764] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:10,765] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003688445.1_ASM368844v1_genomic.fna/markers.fasta)
[2024-01-24 12:45:10,765] [INFO] Task started: Blastn
[2024-01-24 12:45:10,765] [INFO] Running command: blastn -query GCF_003688445.1_ASM368844v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg521f3f55-08e8-4ebc-ae86-7db545dd55ab/dqc_reference/reference_markers_gtdb.fasta -out GCF_003688445.1_ASM368844v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:11,471] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:11,474] [INFO] Selected 14 target genomes.
[2024-01-24 12:45:11,474] [INFO] Target genome list was writen to GCF_003688445.1_ASM368844v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:11,505] [INFO] Task started: fastANI
[2024-01-24 12:45:11,505] [INFO] Running command: fastANI --query /var/lib/cwl/stg71815a7d-a5d5-4bf5-8be6-c2194339beac/GCF_003688445.1_ASM368844v1_genomic.fna.gz --refList GCF_003688445.1_ASM368844v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003688445.1_ASM368844v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:45:14,080] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:14,091] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:45:14,091] [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_003688445.1	s__Metamycoplasma subdolum	100.0	210	211	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000702805.1	s__Metamycoplasma anseris	78.1399	56	211	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900660735.1	s__Metamycoplasma cloacale	77.8524	54	211	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	100.00	100.00	1.00	1.00	3	-
GCF_006385795.1	s__Metamycoplasma falconis	77.8147	50	211	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900660445.2	s__Metamycoplasma salivarium	77.6698	60	211	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:45:14,093] [INFO] GTDB search result was written to GCF_003688445.1_ASM368844v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:45:14,093] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:45:14,096] [INFO] DFAST_QC result json was written to GCF_003688445.1_ASM368844v1_genomic.fna/dqc_result.json
[2024-01-24 12:45:14,097] [INFO] DFAST_QC completed!
[2024-01-24 12:45:14,097] [INFO] Total running time: 0h0m21s