[2023-06-30 16:20:39,439] [INFO] DFAST_QC pipeline started.
[2023-06-30 16:20:39,444] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 16:20:39,444] [INFO] DQC Reference Directory: /var/lib/cwl/stg52c42e18-5e10-405a-88bb-11e8f6c5299b/dqc_reference
[2023-06-30 16:20:41,402] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 16:20:41,403] [INFO] Task started: Prodigal
[2023-06-30 16:20:41,403] [INFO] Running command: gunzip -c /var/lib/cwl/stg9bafa332-5258-457a-914e-9e3dc21bf5f1/GCA_024650045.1_ASM2465004v1_genomic.fna.gz | prodigal -d GCA_024650045.1_ASM2465004v1_genomic.fna/cds.fna -a GCA_024650045.1_ASM2465004v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 16:20:44,638] [INFO] Task succeeded: Prodigal
[2023-06-30 16:20:44,638] [INFO] Task started: HMMsearch
[2023-06-30 16:20:44,638] [INFO] Running command: hmmsearch --tblout GCA_024650045.1_ASM2465004v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg52c42e18-5e10-405a-88bb-11e8f6c5299b/dqc_reference/reference_markers.hmm GCA_024650045.1_ASM2465004v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 16:20:44,810] [INFO] Task succeeded: HMMsearch
[2023-06-30 16:20:44,811] [INFO] Found 6/6 markers.
[2023-06-30 16:20:44,845] [INFO] Query marker FASTA was written to GCA_024650045.1_ASM2465004v1_genomic.fna/markers.fasta
[2023-06-30 16:20:44,846] [INFO] Task started: Blastn
[2023-06-30 16:20:44,846] [INFO] Running command: blastn -query GCA_024650045.1_ASM2465004v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52c42e18-5e10-405a-88bb-11e8f6c5299b/dqc_reference/reference_markers.fasta -out GCA_024650045.1_ASM2465004v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 16:20:46,557] [INFO] Task succeeded: Blastn
[2023-06-30 16:20:46,561] [INFO] Selected 26 target genomes.
[2023-06-30 16:20:46,561] [INFO] Target genome list was writen to GCA_024650045.1_ASM2465004v1_genomic.fna/target_genomes.txt
[2023-06-30 16:20:46,604] [INFO] Task started: fastANI
[2023-06-30 16:20:46,605] [INFO] Running command: fastANI --query /var/lib/cwl/stg9bafa332-5258-457a-914e-9e3dc21bf5f1/GCA_024650045.1_ASM2465004v1_genomic.fna.gz --refList GCA_024650045.1_ASM2465004v1_genomic.fna/target_genomes.txt --output GCA_024650045.1_ASM2465004v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 16:20:53,915] [INFO] Task succeeded: fastANI
[2023-06-30 16:20:53,916] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg52c42e18-5e10-405a-88bb-11e8f6c5299b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 16:20:53,916] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg52c42e18-5e10-405a-88bb-11e8f6c5299b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 16:20:53,922] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 16:20:53,922] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 16:20:53,923] [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
Mariniplasma anaerobium	strain=Mahy22	GCA_016865445.1	2735436	2735436	type	True	77.6744	159	612	95	below_threshold
Alteracholeplasma palmae	strain=J233	GCA_000968055.1	38986	38986	type	True	76.4802	52	612	95	below_threshold
Haploplasma axanthum	strain=NCTC10138	GCA_900660745.1	29552	29552	type	True	76.3073	58	612	95	below_threshold
Haploplasma axanthum	strain=ATCC 25176	GCA_000428705.1	29552	29552	type	True	76.3027	56	612	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 16:20:53,937] [INFO] DFAST Taxonomy check result was written to GCA_024650045.1_ASM2465004v1_genomic.fna/tc_result.tsv
[2023-06-30 16:20:53,938] [INFO] ===== Taxonomy check completed =====
[2023-06-30 16:20:53,938] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 16:20:53,938] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg52c42e18-5e10-405a-88bb-11e8f6c5299b/dqc_reference/checkm_data
[2023-06-30 16:20:53,940] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 16:20:53,960] [INFO] Task started: CheckM
[2023-06-30 16:20:53,961] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024650045.1_ASM2465004v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024650045.1_ASM2465004v1_genomic.fna/checkm_input GCA_024650045.1_ASM2465004v1_genomic.fna/checkm_result
[2023-06-30 16:21:10,905] [INFO] Task succeeded: CheckM
[2023-06-30 16:21:10,906] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 16:21:10,924] [INFO] ===== Completeness check finished =====
[2023-06-30 16:21:10,924] [INFO] ===== Start GTDB Search =====
[2023-06-30 16:21:10,924] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024650045.1_ASM2465004v1_genomic.fna/markers.fasta)
[2023-06-30 16:21:10,925] [INFO] Task started: Blastn
[2023-06-30 16:21:10,925] [INFO] Running command: blastn -query GCA_024650045.1_ASM2465004v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52c42e18-5e10-405a-88bb-11e8f6c5299b/dqc_reference/reference_markers_gtdb.fasta -out GCA_024650045.1_ASM2465004v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 16:21:11,668] [INFO] Task succeeded: Blastn
[2023-06-30 16:21:11,673] [INFO] Selected 14 target genomes.
[2023-06-30 16:21:11,673] [INFO] Target genome list was writen to GCA_024650045.1_ASM2465004v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 16:21:11,679] [INFO] Task started: fastANI
[2023-06-30 16:21:11,679] [INFO] Running command: fastANI --query /var/lib/cwl/stg9bafa332-5258-457a-914e-9e3dc21bf5f1/GCA_024650045.1_ASM2465004v1_genomic.fna.gz --refList GCA_024650045.1_ASM2465004v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024650045.1_ASM2465004v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 16:21:15,926] [INFO] Task succeeded: fastANI
[2023-06-30 16:21:15,938] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 16:21:15,938] [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_002345705.1	s__UBA2284 sp002345705	78.4041	179	612	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__UBA2284	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002839095.1	s__UBA2284 sp002839095	78.3986	227	612	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__UBA2284	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018818645.1	s__UBA2284 sp018818645	78.3317	209	612	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__UBA2284	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002838205.1	s__MZ-XQ sp002838205	78.2984	129	612	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__MZ-XQ	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016934175.1	s__UBA2284 sp016934175	78.0176	120	612	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__UBA2284	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006226985.1	s__UBA2284 sp006226985	77.9239	108	612	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__UBA2284	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001830045.1	s__UBA2284 sp001830045	77.885	131	612	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__UBA2284	95.0	99.91	99.56	0.96	0.85	16	-
GCA_016934015.1	s__UBA6181 sp016934015	77.8203	111	612	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__UBA6181	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018817915.1	s__UBA2284 sp018817915	77.7912	168	612	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__UBA2284	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016865445.1	s__MZ-XQ sp016865445	77.7143	157	612	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__MZ-XQ	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003249785.1	s__UBA2284 sp003249785	77.6029	93	612	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__UBA2284	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002422135.1	s__UBA6181 sp002422135	77.5188	101	612	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__UBA6181	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003518475.1	s__UBA2284 sp003518475	77.4442	86	612	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__UBA2284	95.0	99.36	99.03	0.84	0.83	4	-
GCF_000968055.1	s__Acholeplasma_D palmae	76.5187	51	612	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__Acholeplasma_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 16:21:15,940] [INFO] GTDB search result was written to GCA_024650045.1_ASM2465004v1_genomic.fna/result_gtdb.tsv
[2023-06-30 16:21:15,941] [INFO] ===== GTDB Search completed =====
[2023-06-30 16:21:15,944] [INFO] DFAST_QC result json was written to GCA_024650045.1_ASM2465004v1_genomic.fna/dqc_result.json
[2023-06-30 16:21:15,944] [INFO] DFAST_QC completed!
[2023-06-30 16:21:15,944] [INFO] Total running time: 0h0m37s