[2024-01-24 13:10:19,219] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:10:19,221] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:10:19,221] [INFO] DQC Reference Directory: /var/lib/cwl/stg795b220b-13e8-4cde-b021-243ba265714e/dqc_reference
[2024-01-24 13:10:20,468] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:10:20,469] [INFO] Task started: Prodigal
[2024-01-24 13:10:20,469] [INFO] Running command: gunzip -c /var/lib/cwl/stg95c27290-466a-455c-8f10-f79e36206c5f/GCF_007641255.1_ASM764125v1_genomic.fna.gz | prodigal -d GCF_007641255.1_ASM764125v1_genomic.fna/cds.fna -a GCF_007641255.1_ASM764125v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:34,956] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:34,957] [INFO] Task started: HMMsearch
[2024-01-24 13:10:34,957] [INFO] Running command: hmmsearch --tblout GCF_007641255.1_ASM764125v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg795b220b-13e8-4cde-b021-243ba265714e/dqc_reference/reference_markers.hmm GCF_007641255.1_ASM764125v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:35,346] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:35,349] [INFO] Found 6/6 markers.
[2024-01-24 13:10:35,397] [INFO] Query marker FASTA was written to GCF_007641255.1_ASM764125v1_genomic.fna/markers.fasta
[2024-01-24 13:10:35,397] [INFO] Task started: Blastn
[2024-01-24 13:10:35,397] [INFO] Running command: blastn -query GCF_007641255.1_ASM764125v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg795b220b-13e8-4cde-b021-243ba265714e/dqc_reference/reference_markers.fasta -out GCF_007641255.1_ASM764125v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:36,006] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:36,010] [INFO] Selected 22 target genomes.
[2024-01-24 13:10:36,010] [INFO] Target genome list was writen to GCF_007641255.1_ASM764125v1_genomic.fna/target_genomes.txt
[2024-01-24 13:10:36,018] [INFO] Task started: fastANI
[2024-01-24 13:10:36,018] [INFO] Running command: fastANI --query /var/lib/cwl/stg95c27290-466a-455c-8f10-f79e36206c5f/GCF_007641255.1_ASM764125v1_genomic.fna.gz --refList GCF_007641255.1_ASM764125v1_genomic.fna/target_genomes.txt --output GCF_007641255.1_ASM764125v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:53,489] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:53,490] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg795b220b-13e8-4cde-b021-243ba265714e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:53,490] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg795b220b-13e8-4cde-b021-243ba265714e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:53,506] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:10:53,507] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:53,507] [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
Sporomusa termitida	strain=DSM 4440	GCA_007641255.1	2377	2377	type	True	100.0	1771	1771	95	conclusive
Dendrosporobacter quercicolus	strain=DSM 1736	GCA_013303165.1	146817	146817	type	True	79.415	166	1771	95	below_threshold
Dendrosporobacter quercicolus	strain=DSM 1736	GCA_900104455.1	146817	146817	type	True	79.3358	170	1771	95	below_threshold
Sporomusa malonica	strain=DSM 5090	GCA_900176355.1	112901	112901	type	True	79.1866	566	1771	95	below_threshold
Sporomusa sphaeroides	strain=DSM 2875	GCA_001941975.1	47679	47679	type	True	79.0228	433	1771	95	below_threshold
Sporomusa sphaeroides	strain=DSM 2875	GCA_023660125.1	47679	47679	type	True	78.6591	435	1771	95	below_threshold
Methylomusa anaerophila	strain=MMFC1	GCA_003966895.1	1930071	1930071	type	True	78.1092	147	1771	95	below_threshold
Sporomusa ovata	strain=DSM 2662	GCA_000423685.1	2378	2378	type	True	78.0733	310	1771	95	below_threshold
Sporomusa acidovorans	strain=DSM 3132	GCA_002257695.1	112900	112900	type	True	77.8484	322	1771	95	below_threshold
Sporomusa acidovorans	strain=Mol	GCA_900101845.1	112900	112900	type	True	77.8093	320	1771	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:53,510] [INFO] DFAST Taxonomy check result was written to GCF_007641255.1_ASM764125v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:53,511] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:53,512] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:53,513] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg795b220b-13e8-4cde-b021-243ba265714e/dqc_reference/checkm_data
[2024-01-24 13:10:53,516] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:53,579] [INFO] Task started: CheckM
[2024-01-24 13:10:53,579] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007641255.1_ASM764125v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007641255.1_ASM764125v1_genomic.fna/checkm_input GCF_007641255.1_ASM764125v1_genomic.fna/checkm_result
[2024-01-24 13:11:38,764] [INFO] Task succeeded: CheckM
[2024-01-24 13:11:38,766] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:11:38,791] [INFO] ===== Completeness check finished =====
[2024-01-24 13:11:38,791] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:11:38,792] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007641255.1_ASM764125v1_genomic.fna/markers.fasta)
[2024-01-24 13:11:38,792] [INFO] Task started: Blastn
[2024-01-24 13:11:38,792] [INFO] Running command: blastn -query GCF_007641255.1_ASM764125v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg795b220b-13e8-4cde-b021-243ba265714e/dqc_reference/reference_markers_gtdb.fasta -out GCF_007641255.1_ASM764125v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:11:39,926] [INFO] Task succeeded: Blastn
[2024-01-24 13:11:39,930] [INFO] Selected 23 target genomes.
[2024-01-24 13:11:39,931] [INFO] Target genome list was writen to GCF_007641255.1_ASM764125v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:11:39,956] [INFO] Task started: fastANI
[2024-01-24 13:11:39,956] [INFO] Running command: fastANI --query /var/lib/cwl/stg95c27290-466a-455c-8f10-f79e36206c5f/GCF_007641255.1_ASM764125v1_genomic.fna.gz --refList GCF_007641255.1_ASM764125v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007641255.1_ASM764125v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:55,700] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:55,714] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:11:55,714] [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_007641255.1	s__Sporomusa termitida	100.0	1771	1771	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Sporomusales;f__Sporomusaceae;g__Sporomusa	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900104455.1	s__Dendrosporobacter quercicolus	79.3508	167	1771	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__DSM-1736;f__Dendrosporobacteraceae;g__Dendrosporobacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900176355.1	s__Sporomusa malonica	79.1892	566	1771	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Sporomusales;f__Sporomusaceae;g__Sporomusa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001941975.1	s__Sporomusa sphaeroides	79.016	431	1771	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Sporomusales;f__Sporomusaceae;g__Sporomusa	95.0	98.27	97.38	0.92	0.86	4	-
GCF_000445445.1	s__Sporomusa ovata	78.6991	337	1771	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Sporomusales;f__Sporomusaceae;g__Sporomusa	95.0	99.96	99.93	1.00	0.99	3	-
GCF_003966895.1	s__Methylomusa anaerophila	78.0437	150	1771	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Sporomusales;f__Sporomusaceae;g__Methylomusa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000169155.1	s__Thermosinus carboxydivorans	77.9744	78	1771	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Sporomusales;f__Thermosinaceae;g__Thermosinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101845.1	s__Sporomusa acidovorans	77.7991	320	1771	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Sporomusales;f__Sporomusaceae;g__Sporomusa	95.0	99.98	99.98	0.98	0.98	2	-
GCA_017889705.1	s__Sporomusa sp017889705	77.5619	276	1771	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Sporomusales;f__Sporomusaceae;g__Sporomusa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017889675.1	s__Sporomusa sp017889675	77.4319	162	1771	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Sporomusales;f__Sporomusaceae;g__Sporomusa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001298735.1	s__CYSP01 sp001298735	77.1485	97	1771	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Propionisporales;f__Propionisporaceae;g__CYSP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003990955.1	s__Dendrosporobacter sp003990955	76.9577	97	1771	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__DSM-1736;f__Dendrosporobacteraceae;g__Dendrosporobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900110485.1	s__Propionispora vibrioides	76.8914	105	1771	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Propionisporales;f__Propionisporaceae;g__Propionispora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:11:55,716] [INFO] GTDB search result was written to GCF_007641255.1_ASM764125v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:55,717] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:55,722] [INFO] DFAST_QC result json was written to GCF_007641255.1_ASM764125v1_genomic.fna/dqc_result.json
[2024-01-24 13:11:55,723] [INFO] DFAST_QC completed!
[2024-01-24 13:11:55,723] [INFO] Total running time: 0h1m37s