[2024-01-24 13:40:34,896] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:34,898] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:34,899] [INFO] DQC Reference Directory: /var/lib/cwl/stg3362c5ba-a54e-44e5-a8bd-c6cfebea98db/dqc_reference
[2024-01-24 13:40:36,312] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:36,313] [INFO] Task started: Prodigal
[2024-01-24 13:40:36,313] [INFO] Running command: gunzip -c /var/lib/cwl/stgcf2cc54f-5859-4d26-94e2-9483222ee8e2/GCF_900660755.1_57792_F01-3_genomic.fna.gz | prodigal -d GCF_900660755.1_57792_F01-3_genomic.fna/cds.fna -a GCF_900660755.1_57792_F01-3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:38,842] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:38,842] [INFO] Task started: HMMsearch
[2024-01-24 13:40:38,842] [INFO] Running command: hmmsearch --tblout GCF_900660755.1_57792_F01-3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3362c5ba-a54e-44e5-a8bd-c6cfebea98db/dqc_reference/reference_markers.hmm GCF_900660755.1_57792_F01-3_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:39,119] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:39,120] [INFO] Found 6/6 markers.
[2024-01-24 13:40:39,137] [INFO] Query marker FASTA was written to GCF_900660755.1_57792_F01-3_genomic.fna/markers.fasta
[2024-01-24 13:40:39,137] [INFO] Task started: Blastn
[2024-01-24 13:40:39,137] [INFO] Running command: blastn -query GCF_900660755.1_57792_F01-3_genomic.fna/markers.fasta -db /var/lib/cwl/stg3362c5ba-a54e-44e5-a8bd-c6cfebea98db/dqc_reference/reference_markers.fasta -out GCF_900660755.1_57792_F01-3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:39,705] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:39,708] [INFO] Selected 16 target genomes.
[2024-01-24 13:40:39,708] [INFO] Target genome list was writen to GCF_900660755.1_57792_F01-3_genomic.fna/target_genomes.txt
[2024-01-24 13:40:39,717] [INFO] Task started: fastANI
[2024-01-24 13:40:39,717] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf2cc54f-5859-4d26-94e2-9483222ee8e2/GCF_900660755.1_57792_F01-3_genomic.fna.gz --refList GCF_900660755.1_57792_F01-3_genomic.fna/target_genomes.txt --output GCF_900660755.1_57792_F01-3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:44,645] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:44,645] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3362c5ba-a54e-44e5-a8bd-c6cfebea98db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:44,646] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3362c5ba-a54e-44e5-a8bd-c6cfebea98db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:44,654] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:40:44,654] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:40:44,654] [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
Acholeplasma hippikon	strain=NCTC10172	GCA_900660755.1	264636	264636	type	True	100.0	485	488	95	conclusive
Acholeplasma hippikon	strain=ATCC 29725	GCA_000702765.1	264636	264636	type	True	99.9812	465	488	95	conclusive
Acholeplasma equirhinis	strain=N93	GCA_017052655.1	555393	555393	type	True	78.9777	162	488	95	below_threshold
Acholeplasma granularum	strain=ATCC 19168	GCA_000526235.1	264635	264635	type	True	78.5363	115	488	95	below_threshold
Acholeplasma oculi	strain=NCTC10150	GCA_900444665.1	35623	35623	type	True	78.4686	119	488	95	below_threshold
Acholeplasma equifetale	strain=ATCC 29724	GCA_000687735.1	264634	264634	type	True	78.3758	135	488	95	below_threshold
Acholeplasma oculi	strain=ATCC 27350	GCA_900166985.1	35623	35623	type	True	78.2701	123	488	95	below_threshold
Haploplasma modicum	strain=ATCC 29102	GCA_000687835.1	2150	2150	type	True	76.8826	50	488	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:44,656] [INFO] DFAST Taxonomy check result was written to GCF_900660755.1_57792_F01-3_genomic.fna/tc_result.tsv
[2024-01-24 13:40:44,656] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:44,657] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:44,657] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3362c5ba-a54e-44e5-a8bd-c6cfebea98db/dqc_reference/checkm_data
[2024-01-24 13:40:44,658] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:44,693] [INFO] Task started: CheckM
[2024-01-24 13:40:44,693] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900660755.1_57792_F01-3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900660755.1_57792_F01-3_genomic.fna/checkm_input GCF_900660755.1_57792_F01-3_genomic.fna/checkm_result
[2024-01-24 13:41:01,448] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:01,449] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:01,469] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:01,469] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:01,470] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900660755.1_57792_F01-3_genomic.fna/markers.fasta)
[2024-01-24 13:41:01,470] [INFO] Task started: Blastn
[2024-01-24 13:41:01,470] [INFO] Running command: blastn -query GCF_900660755.1_57792_F01-3_genomic.fna/markers.fasta -db /var/lib/cwl/stg3362c5ba-a54e-44e5-a8bd-c6cfebea98db/dqc_reference/reference_markers_gtdb.fasta -out GCF_900660755.1_57792_F01-3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:02,270] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:02,274] [INFO] Selected 17 target genomes.
[2024-01-24 13:41:02,274] [INFO] Target genome list was writen to GCF_900660755.1_57792_F01-3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:02,287] [INFO] Task started: fastANI
[2024-01-24 13:41:02,287] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf2cc54f-5859-4d26-94e2-9483222ee8e2/GCF_900660755.1_57792_F01-3_genomic.fna.gz --refList GCF_900660755.1_57792_F01-3_genomic.fna/target_genomes_gtdb.txt --output GCF_900660755.1_57792_F01-3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:06,968] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:06,978] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:06,979] [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_900660755.1	s__Acholeplasma hippikon	100.0	485	488	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__Acholeplasma	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_017052655.1	s__Acholeplasma equirhinis	79.0175	160	488	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__Acholeplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000526235.1	s__Acholeplasma granularum	78.5395	115	488	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__Acholeplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015709225.1	s__Acholeplasma laidlawii_A	78.48	103	488	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__Acholeplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000687735.1	s__Acholeplasma equifetale	78.3901	135	488	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__Acholeplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000018785.1	s__Acholeplasma laidlawii	78.2824	107	488	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__Acholeplasma	95.0	99.83	98.26	1.00	1.00	15	-
GCF_900166985.1	s__Acholeplasma oculi	78.2811	122	488	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__Acholeplasma	95.0	99.99	99.99	0.99	0.99	3	-
GCA_002399815.1	s__Acholeplasma sp002399815	78.0979	125	488	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__Acholeplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000968055.1	s__Acholeplasma_D palmae	77.7259	59	488	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__Acholeplasma_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000687835.1	s__Acholeplasma_A modicum	76.8399	51	488	d__Bacteria;p__Firmicutes;c__Bacilli;o__Acholeplasmatales;f__Acholeplasmataceae;g__Acholeplasma_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:06,981] [INFO] GTDB search result was written to GCF_900660755.1_57792_F01-3_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:06,981] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:06,985] [INFO] DFAST_QC result json was written to GCF_900660755.1_57792_F01-3_genomic.fna/dqc_result.json
[2024-01-24 13:41:06,986] [INFO] DFAST_QC completed!
[2024-01-24 13:41:06,986] [INFO] Total running time: 0h0m32s