[2024-01-24 12:47:05,349] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:05,351] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:05,351] [INFO] DQC Reference Directory: /var/lib/cwl/stgfe789b76-5536-4959-b4a8-ea11749c5381/dqc_reference
[2024-01-24 12:47:06,502] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:06,511] [INFO] Task started: Prodigal
[2024-01-24 12:47:06,511] [INFO] Running command: gunzip -c /var/lib/cwl/stg3f858fa3-08b0-4c73-abe7-80a4fcd23a1d/GCF_000008765.1_ASM876v1_genomic.fna.gz | prodigal -d GCF_000008765.1_ASM876v1_genomic.fna/cds.fna -a GCF_000008765.1_ASM876v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:13,431] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:13,431] [INFO] Task started: HMMsearch
[2024-01-24 12:47:13,431] [INFO] Running command: hmmsearch --tblout GCF_000008765.1_ASM876v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfe789b76-5536-4959-b4a8-ea11749c5381/dqc_reference/reference_markers.hmm GCF_000008765.1_ASM876v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:13,684] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:13,686] [INFO] Found 6/6 markers.
[2024-01-24 12:47:13,718] [INFO] Query marker FASTA was written to GCF_000008765.1_ASM876v1_genomic.fna/markers.fasta
[2024-01-24 12:47:13,719] [INFO] Task started: Blastn
[2024-01-24 12:47:13,719] [INFO] Running command: blastn -query GCF_000008765.1_ASM876v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe789b76-5536-4959-b4a8-ea11749c5381/dqc_reference/reference_markers.fasta -out GCF_000008765.1_ASM876v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:14,294] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:14,297] [INFO] Selected 11 target genomes.
[2024-01-24 12:47:14,297] [INFO] Target genome list was writen to GCF_000008765.1_ASM876v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:14,303] [INFO] Task started: fastANI
[2024-01-24 12:47:14,303] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f858fa3-08b0-4c73-abe7-80a4fcd23a1d/GCF_000008765.1_ASM876v1_genomic.fna.gz --refList GCF_000008765.1_ASM876v1_genomic.fna/target_genomes.txt --output GCF_000008765.1_ASM876v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:23,654] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:23,654] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfe789b76-5536-4959-b4a8-ea11749c5381/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:23,654] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfe789b76-5536-4959-b4a8-ea11749c5381/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:23,663] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:47:23,664] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:23,664] [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 acetobutylicum	strain=ATCC 824	GCA_000008765.1	1488	1488	type	True	100.0	1376	1377	95	conclusive
Clostridium felsineum	strain=DSM 793	GCA_002006235.2	36839	36839	type	True	82.8562	934	1377	95	below_threshold
Clostridium felsineum	strain=DSM 794	GCA_002006355.2	36839	36839	type	True	82.8007	953	1377	95	below_threshold
Clostridium felsineum	strain=DSM 7320	GCA_002006215.2	36839	36839	type	True	82.8005	928	1377	95	below_threshold
Clostridium hydrogenum	strain=CUEA01	GCA_021432385.1	2855764	2855764	type	True	78.5098	323	1377	95	below_threshold
Clostridium mobile	strain=MSJ-11	GCA_018918285.1	2841512	2841512	type	True	76.3571	111	1377	95	below_threshold
Clostridium tarantellae	strain=DSM 3997	GCA_009295725.1	39493	39493	type	True	76.0273	116	1377	95	below_threshold
Clostridium acetireducens	strain=DSM 10703	GCA_001758365.1	76489	76489	type	True	75.9703	118	1377	95	below_threshold
Clostridium senegalense	strain=type strain: JC122	GCA_000285575.1	1465809	1465809	type	True	75.8862	140	1377	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:23,666] [INFO] DFAST Taxonomy check result was written to GCF_000008765.1_ASM876v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:23,667] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:23,667] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:23,667] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfe789b76-5536-4959-b4a8-ea11749c5381/dqc_reference/checkm_data
[2024-01-24 12:47:23,668] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:23,711] [INFO] Task started: CheckM
[2024-01-24 12:47:23,712] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000008765.1_ASM876v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000008765.1_ASM876v1_genomic.fna/checkm_input GCF_000008765.1_ASM876v1_genomic.fna/checkm_result
[2024-01-24 12:47:50,107] [INFO] Task succeeded: CheckM
[2024-01-24 12:47:50,108] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:47:50,129] [INFO] ===== Completeness check finished =====
[2024-01-24 12:47:50,129] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:47:50,130] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000008765.1_ASM876v1_genomic.fna/markers.fasta)
[2024-01-24 12:47:50,130] [INFO] Task started: Blastn
[2024-01-24 12:47:50,130] [INFO] Running command: blastn -query GCF_000008765.1_ASM876v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe789b76-5536-4959-b4a8-ea11749c5381/dqc_reference/reference_markers_gtdb.fasta -out GCF_000008765.1_ASM876v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:50,859] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:50,862] [INFO] Selected 15 target genomes.
[2024-01-24 12:47:50,862] [INFO] Target genome list was writen to GCF_000008765.1_ASM876v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:47:50,885] [INFO] Task started: fastANI
[2024-01-24 12:47:50,886] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f858fa3-08b0-4c73-abe7-80a4fcd23a1d/GCF_000008765.1_ASM876v1_genomic.fna.gz --refList GCF_000008765.1_ASM876v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000008765.1_ASM876v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:01,062] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:01,075] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:48:01,075] [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_000008765.1	s__Clostridium_S acetobutylicum	100.0	1376	1377	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_S	95.0	99.88	98.04	0.99	0.94	19	conclusive
GCF_002006355.1	s__Clostridium_S felsineum	82.6335	922	1377	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_S	95.0	98.29	98.24	0.88	0.87	4	-
GCF_001705235.1	s__Clostridium_S pasteurianum_A	80.4544	627	1377	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_S	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001270375.1	s__Clostridium_S sp001270375	77.8751	287	1377	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_S	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003718715.1	s__JN-1 sp003718715	77.5644	140	1377	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__JN-1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000389635.1	s__Clostridium_I pasteurianum_A	77.5317	188	1377	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014050525.1	s__Clostridium_B sp014050525	76.6563	120	1377	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000686725.1	s__Clostridium_I akagii	76.5434	162	1377	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_I	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000753455.2	s__Clostridium sp000753455	76.5045	96	1377	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.13	99.13	0.91	0.91	2	-
GCF_900167505.1	s__F0540 sp900167505	76.2248	130	1377	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__F0540	95.0	98.87	98.87	0.90	0.90	2	-
GCF_900290265.1	s__Clostridium cagae	76.2004	133	1377	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_009295725.1	s__Clostridium_P tarantellae	76.0273	116	1377	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001758365.1	s__Clostridium_C acetireducens	75.9443	120	1377	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000285575.1	s__Clostridium_J senegalense	75.8868	140	1377	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J	95.0	97.19	95.52	0.93	0.91	5	-
GCA_002455975.1	s__Clostridium_J sp002455975	75.6305	96	1377	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:48:01,077] [INFO] GTDB search result was written to GCF_000008765.1_ASM876v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:01,077] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:01,095] [INFO] DFAST_QC result json was written to GCF_000008765.1_ASM876v1_genomic.fna/dqc_result.json
[2024-01-24 12:48:01,095] [INFO] DFAST_QC completed!
[2024-01-24 12:48:01,095] [INFO] Total running time: 0h0m56s