[2024-01-24 12:53:39,618] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:39,620] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:39,620] [INFO] DQC Reference Directory: /var/lib/cwl/stg24a69f4d-023c-4bfe-90dc-6dba09b46c1f/dqc_reference
[2024-01-24 12:53:40,977] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:40,979] [INFO] Task started: Prodigal
[2024-01-24 12:53:40,979] [INFO] Running command: gunzip -c /var/lib/cwl/stg03199a22-03c7-478d-8c61-ea6305efea83/GCF_000196455.1_ASM19645v1_genomic.fna.gz | prodigal -d GCF_000196455.1_ASM19645v1_genomic.fna/cds.fna -a GCF_000196455.1_ASM19645v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:53:45,862] [INFO] Task succeeded: Prodigal
[2024-01-24 12:53:45,862] [INFO] Task started: HMMsearch
[2024-01-24 12:53:45,862] [INFO] Running command: hmmsearch --tblout GCF_000196455.1_ASM19645v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg24a69f4d-023c-4bfe-90dc-6dba09b46c1f/dqc_reference/reference_markers.hmm GCF_000196455.1_ASM19645v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:53:46,251] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:53:46,252] [INFO] Found 6/6 markers.
[2024-01-24 12:53:46,293] [INFO] Query marker FASTA was written to GCF_000196455.1_ASM19645v1_genomic.fna/markers.fasta
[2024-01-24 12:53:46,293] [INFO] Task started: Blastn
[2024-01-24 12:53:46,293] [INFO] Running command: blastn -query GCF_000196455.1_ASM19645v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24a69f4d-023c-4bfe-90dc-6dba09b46c1f/dqc_reference/reference_markers.fasta -out GCF_000196455.1_ASM19645v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:47,940] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:47,944] [INFO] Selected 16 target genomes.
[2024-01-24 12:53:47,945] [INFO] Target genome list was writen to GCF_000196455.1_ASM19645v1_genomic.fna/target_genomes.txt
[2024-01-24 12:53:47,952] [INFO] Task started: fastANI
[2024-01-24 12:53:47,952] [INFO] Running command: fastANI --query /var/lib/cwl/stg03199a22-03c7-478d-8c61-ea6305efea83/GCF_000196455.1_ASM19645v1_genomic.fna.gz --refList GCF_000196455.1_ASM19645v1_genomic.fna/target_genomes.txt --output GCF_000196455.1_ASM19645v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:53:56,315] [INFO] Task succeeded: fastANI
[2024-01-24 12:53:56,316] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg24a69f4d-023c-4bfe-90dc-6dba09b46c1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:53:56,316] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg24a69f4d-023c-4bfe-90dc-6dba09b46c1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:53:56,384] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:53:56,384] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:53:56,385] [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
Acetoanaerobium sticklandii	strain=DSM 519	GCA_000196455.1	1511	1511	type	True	100.0	905	905	95	inconclusive
Acetoanaerobium noterae	strain=ATCC 35199	GCA_900168025.1	745369	745369	type	True	96.2259	782	905	95	inconclusive
Romboutsia hominis	strain=FRIFI	GCA_900002575.1	1507512	1507512	type	True	78.9101	59	905	95	below_threshold
Acetoanaerobium pronyense	strain=DSM 27512	GCA_017874355.1	1482736	1482736	type	True	77.8311	163	905	95	below_threshold
Paeniclostridium sordellii	strain=ATCC9714	GCA_000953675.1	1505	1505	type	True	76.3336	54	905	95	below_threshold
Terrisporobacter othiniensis	strain=08-306576	GCA_000808015.1	1577792	1577792	type	True	76.1366	52	905	95	below_threshold
Tepidibacter formicigenes	strain=DSM 15518	GCA_900142235.1	227138	227138	type	True	75.9771	85	905	95	below_threshold
Paraclostridium bifermentans	strain=ATCC 638	GCA_006802875.1	1490	1490	type	True	75.8256	54	905	95	below_threshold
Terrisporobacter glycolicus	strain=DSM 1288	GCA_000439105.1	36841	36841	suspected-type	True	75.6304	58	905	95	below_threshold
Terrisporobacter glycolicus	strain=ATCC 14880	GCA_000373865.1	36841	36841	suspected-type	True	75.4668	58	905	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:53:56,386] [INFO] DFAST Taxonomy check result was written to GCF_000196455.1_ASM19645v1_genomic.fna/tc_result.tsv
[2024-01-24 12:53:56,387] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:53:56,387] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:53:56,387] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg24a69f4d-023c-4bfe-90dc-6dba09b46c1f/dqc_reference/checkm_data
[2024-01-24 12:53:56,393] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:53:56,428] [INFO] Task started: CheckM
[2024-01-24 12:53:56,428] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000196455.1_ASM19645v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000196455.1_ASM19645v1_genomic.fna/checkm_input GCF_000196455.1_ASM19645v1_genomic.fna/checkm_result
[2024-01-24 12:54:19,496] [INFO] Task succeeded: CheckM
[2024-01-24 12:54:19,497] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:54:19,521] [INFO] ===== Completeness check finished =====
[2024-01-24 12:54:19,521] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:54:19,521] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000196455.1_ASM19645v1_genomic.fna/markers.fasta)
[2024-01-24 12:54:19,522] [INFO] Task started: Blastn
[2024-01-24 12:54:19,522] [INFO] Running command: blastn -query GCF_000196455.1_ASM19645v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24a69f4d-023c-4bfe-90dc-6dba09b46c1f/dqc_reference/reference_markers_gtdb.fasta -out GCF_000196455.1_ASM19645v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:20,356] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:20,361] [INFO] Selected 15 target genomes.
[2024-01-24 12:54:20,361] [INFO] Target genome list was writen to GCF_000196455.1_ASM19645v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:54:20,394] [INFO] Task started: fastANI
[2024-01-24 12:54:20,394] [INFO] Running command: fastANI --query /var/lib/cwl/stg03199a22-03c7-478d-8c61-ea6305efea83/GCF_000196455.1_ASM19645v1_genomic.fna.gz --refList GCF_000196455.1_ASM19645v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000196455.1_ASM19645v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:54:27,884] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:27,909] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:54:27,910] [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_000196455.1	s__Acetoanaerobium sticklandii	100.0	905	905	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Filifactoraceae;g__Acetoanaerobium	96.3037	N/A	N/A	N/A	N/A	1	conclusive
GCF_900168025.1	s__Acetoanaerobium noterae	96.2259	782	905	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Filifactoraceae;g__Acetoanaerobium	96.3037	98.02	97.03	0.90	0.82	5	-
GCF_900002575.1	s__Romboutsia_C hominis	78.2135	54	905	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Romboutsia_C	95.0	98.29	95.25	0.93	0.90	6	-
GCF_017874355.1	s__Acetoanaerobium pronyense	77.8109	164	905	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Filifactoraceae;g__Acetoanaerobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000953675.1	s__Paraclostridium sordellii	76.3307	54	905	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Paraclostridium	95.0	98.12	96.78	0.93	0.89	59	-
GCF_000808015.1	s__Terrisporobacter othiniensis	76.1366	52	905	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Terrisporobacter	95.0	99.48	99.45	0.91	0.90	3	-
GCF_900142235.1	s__Tepidibacter formicigenes	75.9771	85	905	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Tepidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006802875.1	s__Paraclostridium bifermentans	75.8256	54	905	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Paraclostridium	96.2286	97.64	96.79	0.90	0.86	14	-
GCF_000439105.1	s__Terrisporobacter glycolicus	75.6304	58	905	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Terrisporobacter	95.0	99.67	99.35	0.98	0.96	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:54:27,913] [INFO] GTDB search result was written to GCF_000196455.1_ASM19645v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:54:27,913] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:54:27,916] [INFO] DFAST_QC result json was written to GCF_000196455.1_ASM19645v1_genomic.fna/dqc_result.json
[2024-01-24 12:54:27,916] [INFO] DFAST_QC completed!
[2024-01-24 12:54:27,916] [INFO] Total running time: 0h0m48s