[2024-01-24 11:19:53,699] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:19:53,701] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:19:53,702] [INFO] DQC Reference Directory: /var/lib/cwl/stg4fdfa856-b972-4444-8d85-d32046a86eb5/dqc_reference
[2024-01-24 11:19:55,085] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:19:55,086] [INFO] Task started: Prodigal
[2024-01-24 11:19:55,086] [INFO] Running command: gunzip -c /var/lib/cwl/stg16e7d897-fa1b-48a4-9fb0-4d21002360b0/GCF_019977655.1_ASM1997765v1_genomic.fna.gz | prodigal -d GCF_019977655.1_ASM1997765v1_genomic.fna/cds.fna -a GCF_019977655.1_ASM1997765v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:04,959] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:04,960] [INFO] Task started: HMMsearch
[2024-01-24 11:20:04,960] [INFO] Running command: hmmsearch --tblout GCF_019977655.1_ASM1997765v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4fdfa856-b972-4444-8d85-d32046a86eb5/dqc_reference/reference_markers.hmm GCF_019977655.1_ASM1997765v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:05,329] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:05,330] [INFO] Found 6/6 markers.
[2024-01-24 11:20:05,374] [INFO] Query marker FASTA was written to GCF_019977655.1_ASM1997765v1_genomic.fna/markers.fasta
[2024-01-24 11:20:05,375] [INFO] Task started: Blastn
[2024-01-24 11:20:05,375] [INFO] Running command: blastn -query GCF_019977655.1_ASM1997765v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4fdfa856-b972-4444-8d85-d32046a86eb5/dqc_reference/reference_markers.fasta -out GCF_019977655.1_ASM1997765v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:06,005] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:06,009] [INFO] Selected 19 target genomes.
[2024-01-24 11:20:06,010] [INFO] Target genome list was writen to GCF_019977655.1_ASM1997765v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:06,017] [INFO] Task started: fastANI
[2024-01-24 11:20:06,018] [INFO] Running command: fastANI --query /var/lib/cwl/stg16e7d897-fa1b-48a4-9fb0-4d21002360b0/GCF_019977655.1_ASM1997765v1_genomic.fna.gz --refList GCF_019977655.1_ASM1997765v1_genomic.fna/target_genomes.txt --output GCF_019977655.1_ASM1997765v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:24,859] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:24,860] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4fdfa856-b972-4444-8d85-d32046a86eb5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:24,860] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4fdfa856-b972-4444-8d85-d32046a86eb5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:24,877] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:20:24,877] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:20:24,877] [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 gelidum	strain=C5S11	GCA_019977655.1	704125	704125	type	True	100.0	2012	2013	95	conclusive
Clostridium puniceum	strain=DSM 2619	GCA_002006345.1	29367	29367	type	True	83.6434	1010	2013	95	below_threshold
Clostridium diolis	strain=DSM 15410	GCA_008705175.1	223919	223919	suspected-type	True	81.2866	924	2013	95	below_threshold
Clostridium beijerinckii	strain=DSM 791	GCA_018223745.1	1520	1520	suspected-type	True	81.2578	951	2013	95	below_threshold
Clostridium beijerinckii	strain=DSM 791	GCA_002006445.1	1520	1520	suspected-type	True	81.1182	881	2013	95	below_threshold
Clostridium saccharobutylicum	strain=DSM 13864	GCA_000473995.1	169679	169679	type	True	81.0704	869	2013	95	below_threshold
Clostridium saccharoperbutylacetonicum	strain=N1-4(HMT)	GCA_000340885.1	36745	36745	type	True	80.9186	957	2013	95	below_threshold
Clostridium saccharobutylicum	strain=DSM 13864	GCA_001657435.1	169679	169679	type	True	80.8544	783	2013	95	below_threshold
Clostridium saccharoperbutylacetonicum	strain=ATCC 27021	GCA_000334435.1	36745	36745	type	True	80.7201	933	2013	95	below_threshold
Clostridium cibarium	strain=Sa3CVN1	GCA_014836335.1	2762247	2762247	type	True	77.5859	350	2013	95	below_threshold
Clostridium nigeriense	strain=Marseille-P2414	GCA_900086595.1	1805470	1805470	type	True	77.4956	261	2013	95	below_threshold
Clostridium moniliforme	strain=DSM 3984	GCA_017873235.1	39489	39489	type	True	77.1833	250	2013	95	below_threshold
Clostridium sardiniense	strain=DSM 2632	GCA_016907995.1	29369	29369	type	True	77.0637	270	2013	95	below_threshold
Clostridium mediterraneense	strain=Marseille-P2434	GCA_900091705.1	1805472	1805472	type	True	77.0325	197	2013	95	below_threshold
Clostridium muellerianum	strain=P21	GCA_012926525.1	2716538	2716538	type	True	76.7651	258	2013	95	below_threshold
Clostridium tertium	strain=DSM 2485	GCA_017873245.1	1559	1559	type	True	76.7625	270	2013	95	below_threshold
Hathewaya massiliensis	strain=Marseille-P3545	GCA_902143515.1	1964382	1964382	type	True	76.5975	135	2013	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:24,879] [INFO] DFAST Taxonomy check result was written to GCF_019977655.1_ASM1997765v1_genomic.fna/tc_result.tsv
[2024-01-24 11:20:24,880] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:24,880] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:24,880] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4fdfa856-b972-4444-8d85-d32046a86eb5/dqc_reference/checkm_data
[2024-01-24 11:20:24,881] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:24,945] [INFO] Task started: CheckM
[2024-01-24 11:20:24,945] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019977655.1_ASM1997765v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019977655.1_ASM1997765v1_genomic.fna/checkm_input GCF_019977655.1_ASM1997765v1_genomic.fna/checkm_result
[2024-01-24 11:20:59,540] [INFO] Task succeeded: CheckM
[2024-01-24 11:20:59,542] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:20:59,564] [INFO] ===== Completeness check finished =====
[2024-01-24 11:20:59,564] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:20:59,564] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019977655.1_ASM1997765v1_genomic.fna/markers.fasta)
[2024-01-24 11:20:59,565] [INFO] Task started: Blastn
[2024-01-24 11:20:59,565] [INFO] Running command: blastn -query GCF_019977655.1_ASM1997765v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4fdfa856-b972-4444-8d85-d32046a86eb5/dqc_reference/reference_markers_gtdb.fasta -out GCF_019977655.1_ASM1997765v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:00,340] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:00,343] [INFO] Selected 14 target genomes.
[2024-01-24 11:21:00,343] [INFO] Target genome list was writen to GCF_019977655.1_ASM1997765v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:21:00,349] [INFO] Task started: fastANI
[2024-01-24 11:21:00,349] [INFO] Running command: fastANI --query /var/lib/cwl/stg16e7d897-fa1b-48a4-9fb0-4d21002360b0/GCF_019977655.1_ASM1997765v1_genomic.fna.gz --refList GCF_019977655.1_ASM1997765v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019977655.1_ASM1997765v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:21:15,568] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:15,583] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:21:15,583] [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_003129525.1	s__Clostridium beijerinckii_D	87.0011	993	2013	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	83.6463	1010	2013	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_009928485.1	s__Clostridium sp009928485	81.5032	1026	2013	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_018223745.1	s__Clostridium beijerinckii	81.2475	951	2013	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	97.01	95.18	0.85	0.79	244	-
GCF_000473995.1	s__Clostridium saccharobutylicum	81.0877	864	2013	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_002760435.1	s__Clostridium sp002760435	81.0801	944	2013	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.99	99.99	0.98	0.98	2	-
GCF_000621745.1	s__Clostridium beijerinckii_A	81.0471	934	2013	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_000230835.1	s__Clostridium sp000230835	81.0377	921	2013	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_000340885.1	s__Clostridium saccharoperbutylacetonicum	80.9161	961	2013	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_001735765.2	s__Clostridium taeniosporum	78.6964	457	2013	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_017873235.1	s__Clostridium moniliforme	77.1644	247	2013	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_902143515.1	s__Hathewaya massiliensis	76.6064	135	2013	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Hathewaya	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900540255.1	s__Clostridium sp900540255	76.4949	255	2013	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.08	99.08	0.90	0.89	4	-
--------------------------------------------------------------------------------
[2024-01-24 11:21:15,585] [INFO] GTDB search result was written to GCF_019977655.1_ASM1997765v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:21:15,586] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:21:15,589] [INFO] DFAST_QC result json was written to GCF_019977655.1_ASM1997765v1_genomic.fna/dqc_result.json
[2024-01-24 11:21:15,589] [INFO] DFAST_QC completed!
[2024-01-24 11:21:15,589] [INFO] Total running time: 0h1m22s