[2024-01-24 13:09:44,522] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:44,526] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:44,526] [INFO] DQC Reference Directory: /var/lib/cwl/stg76590d62-18ea-4f08-9faf-fa9f8fe4b58f/dqc_reference
[2024-01-24 13:09:45,851] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:45,852] [INFO] Task started: Prodigal
[2024-01-24 13:09:45,853] [INFO] Running command: gunzip -c /var/lib/cwl/stgf325672f-d1d6-4f77-9ce3-f73e133ffaa0/GCF_002006445.1_ASM200644v1_genomic.fna.gz | prodigal -d GCF_002006445.1_ASM200644v1_genomic.fna/cds.fna -a GCF_002006445.1_ASM200644v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:54,393] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:54,393] [INFO] Task started: HMMsearch
[2024-01-24 13:09:54,393] [INFO] Running command: hmmsearch --tblout GCF_002006445.1_ASM200644v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg76590d62-18ea-4f08-9faf-fa9f8fe4b58f/dqc_reference/reference_markers.hmm GCF_002006445.1_ASM200644v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:54,769] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:54,770] [INFO] Found 6/6 markers.
[2024-01-24 13:09:54,814] [INFO] Query marker FASTA was written to GCF_002006445.1_ASM200644v1_genomic.fna/markers.fasta
[2024-01-24 13:09:54,814] [INFO] Task started: Blastn
[2024-01-24 13:09:54,814] [INFO] Running command: blastn -query GCF_002006445.1_ASM200644v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg76590d62-18ea-4f08-9faf-fa9f8fe4b58f/dqc_reference/reference_markers.fasta -out GCF_002006445.1_ASM200644v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:55,445] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:55,448] [INFO] Selected 15 target genomes.
[2024-01-24 13:09:55,448] [INFO] Target genome list was writen to GCF_002006445.1_ASM200644v1_genomic.fna/target_genomes.txt
[2024-01-24 13:09:55,453] [INFO] Task started: fastANI
[2024-01-24 13:09:55,454] [INFO] Running command: fastANI --query /var/lib/cwl/stgf325672f-d1d6-4f77-9ce3-f73e133ffaa0/GCF_002006445.1_ASM200644v1_genomic.fna.gz --refList GCF_002006445.1_ASM200644v1_genomic.fna/target_genomes.txt --output GCF_002006445.1_ASM200644v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:14,513] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:14,514] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg76590d62-18ea-4f08-9faf-fa9f8fe4b58f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:14,514] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg76590d62-18ea-4f08-9faf-fa9f8fe4b58f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:14,525] [INFO] Found 13 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 13:10:14,526] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:10:14,526] [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
Clostridium beijerinckii	strain=DSM 791	GCA_002006445.1	1520	1520	suspected-type	True	100.0	1788	1803	95	inconclusive
Clostridium beijerinckii	strain=DSM 791	GCA_018223745.1	1520	1520	suspected-type	True	99.9952	1803	1803	95	inconclusive
Clostridium beijerinckii	strain=NCTC13035	GCA_900447025.1	1520	1520	suspected-type	True	99.9933	1794	1803	95	inconclusive
Clostridium diolis	strain=DSM 15410	GCA_008580445.1	223919	223919	suspected-type	True	98.2692	1607	1803	95	inconclusive
Clostridium diolis	strain=DSM 15410	GCA_008705175.1	223919	223919	suspected-type	True	98.2136	1623	1803	95	inconclusive
Clostridium gelidum	strain=C5S11	GCA_019977655.1	704125	704125	type	True	81.0488	898	1803	95	below_threshold
Clostridium butyricum	strain=NBRC 13949	GCA_006742065.1	1492	1492	type	True	78.9587	480	1803	95	below_threshold
Clostridium butyricum	strain=DSM 10702	GCA_014131795.1	1492	1492	type	True	78.8472	475	1803	95	below_threshold
Clostridium butyricum	strain=NBRC 13949	GCA_007992895.1	1492	1492	type	True	78.7418	453	1803	95	below_threshold
Clostridium butyricum	strain=DSM 10702	GCA_000409755.1	1492	1492	type	True	78.6682	453	1803	95	below_threshold
Clostridium cagae	strain=Marseille-P4344	GCA_900290265.1	2080751	2080751	type	True	78.6614	389	1803	95	below_threshold
Clostridium weizhouense	strain=YB-6	GCA_019431045.1	2859781	2859781	type	True	78.4709	446	1803	95	below_threshold
Aquimarina latercula	strain=DSM 2041	GCA_000430645.1	987	987	type	True	74.6392	51	1803	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:14,528] [INFO] DFAST Taxonomy check result was written to GCF_002006445.1_ASM200644v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:14,528] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:14,528] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:14,529] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg76590d62-18ea-4f08-9faf-fa9f8fe4b58f/dqc_reference/checkm_data
[2024-01-24 13:10:14,530] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:14,585] [INFO] Task started: CheckM
[2024-01-24 13:10:14,586] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002006445.1_ASM200644v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002006445.1_ASM200644v1_genomic.fna/checkm_input GCF_002006445.1_ASM200644v1_genomic.fna/checkm_result
[2024-01-24 13:10:46,708] [INFO] Task succeeded: CheckM
[2024-01-24 13:10:46,710] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:10:46,727] [INFO] ===== Completeness check finished =====
[2024-01-24 13:10:46,728] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:10:46,728] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002006445.1_ASM200644v1_genomic.fna/markers.fasta)
[2024-01-24 13:10:46,728] [INFO] Task started: Blastn
[2024-01-24 13:10:46,729] [INFO] Running command: blastn -query GCF_002006445.1_ASM200644v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg76590d62-18ea-4f08-9faf-fa9f8fe4b58f/dqc_reference/reference_markers_gtdb.fasta -out GCF_002006445.1_ASM200644v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:47,559] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:47,563] [INFO] Selected 13 target genomes.
[2024-01-24 13:10:47,563] [INFO] Target genome list was writen to GCF_002006445.1_ASM200644v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:10:47,566] [INFO] Task started: fastANI
[2024-01-24 13:10:47,566] [INFO] Running command: fastANI --query /var/lib/cwl/stgf325672f-d1d6-4f77-9ce3-f73e133ffaa0/GCF_002006445.1_ASM200644v1_genomic.fna.gz --refList GCF_002006445.1_ASM200644v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002006445.1_ASM200644v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:04,959] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:04,970] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:11:04,971] [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_018223745.1	s__Clostridium beijerinckii	99.9952	1803	1803	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	97.01	95.18	0.85	0.79	244	conclusive
GCF_000621745.1	s__Clostridium beijerinckii_A	92.3071	1470	1803	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002029255.1	s__Clostridium chromiireducens	82.7047	960	1803	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.07	97.40	0.90	0.87	3	-
GCF_000230835.1	s__Clostridium sp000230835	81.7073	974	1803	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	96.12	96.12	0.82	0.82	2	-
GCF_002760435.1	s__Clostridium sp002760435	81.6541	927	1803	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.99	99.99	0.98	0.98	2	-
GCA_003129525.1	s__Clostridium beijerinckii_D	81.5073	812	1803	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002006345.1	s__Clostridium puniceum	80.9242	811	1803	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000340885.1	s__Clostridium saccharoperbutylacetonicum	80.8625	849	1803	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.35	98.00	0.96	0.89	7	-
GCF_000473995.1	s__Clostridium saccharobutylicum	80.6271	728	1803	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.89	95.82	0.99	0.83	65	-
GCF_009928485.1	s__Clostridium sp009928485	80.4835	799	1803	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006742065.1	s__Clostridium butyricum	78.9415	478	1803	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.58	97.46	0.89	0.80	64	-
GCF_900290265.1	s__Clostridium cagae	78.6641	387	1803	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.09	97.56	0.90	0.85	15	-
GCF_001735765.2	s__Clostridium taeniosporum	78.4417	385	1803	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:11:05,005] [INFO] GTDB search result was written to GCF_002006445.1_ASM200644v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:05,006] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:05,009] [INFO] DFAST_QC result json was written to GCF_002006445.1_ASM200644v1_genomic.fna/dqc_result.json
[2024-01-24 13:11:05,010] [INFO] DFAST_QC completed!
[2024-01-24 13:11:05,010] [INFO] Total running time: 0h1m20s