[2024-01-25 17:52:50,232] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:52:50,233] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:52:50,233] [INFO] DQC Reference Directory: /var/lib/cwl/stg27937e2e-09b3-4474-a9a2-1089da344901/dqc_reference
[2024-01-25 17:52:51,379] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:52:51,380] [INFO] Task started: Prodigal
[2024-01-25 17:52:51,380] [INFO] Running command: gunzip -c /var/lib/cwl/stg1e3efd02-11dd-4fa1-a187-8b667b917f0f/GCF_002006355.2_ASM200635v2_genomic.fna.gz | prodigal -d GCF_002006355.2_ASM200635v2_genomic.fna/cds.fna -a GCF_002006355.2_ASM200635v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:52:58,972] [INFO] Task succeeded: Prodigal
[2024-01-25 17:52:58,972] [INFO] Task started: HMMsearch
[2024-01-25 17:52:58,972] [INFO] Running command: hmmsearch --tblout GCF_002006355.2_ASM200635v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg27937e2e-09b3-4474-a9a2-1089da344901/dqc_reference/reference_markers.hmm GCF_002006355.2_ASM200635v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:52:59,244] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:52:59,245] [INFO] Found 6/6 markers.
[2024-01-25 17:52:59,284] [INFO] Query marker FASTA was written to GCF_002006355.2_ASM200635v2_genomic.fna/markers.fasta
[2024-01-25 17:52:59,284] [INFO] Task started: Blastn
[2024-01-25 17:52:59,284] [INFO] Running command: blastn -query GCF_002006355.2_ASM200635v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg27937e2e-09b3-4474-a9a2-1089da344901/dqc_reference/reference_markers.fasta -out GCF_002006355.2_ASM200635v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:52:59,820] [INFO] Task succeeded: Blastn
[2024-01-25 17:52:59,825] [INFO] Selected 8 target genomes.
[2024-01-25 17:52:59,825] [INFO] Target genome list was writen to GCF_002006355.2_ASM200635v2_genomic.fna/target_genomes.txt
[2024-01-25 17:52:59,833] [INFO] Task started: fastANI
[2024-01-25 17:52:59,833] [INFO] Running command: fastANI --query /var/lib/cwl/stg1e3efd02-11dd-4fa1-a187-8b667b917f0f/GCF_002006355.2_ASM200635v2_genomic.fna.gz --refList GCF_002006355.2_ASM200635v2_genomic.fna/target_genomes.txt --output GCF_002006355.2_ASM200635v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:53:09,425] [INFO] Task succeeded: fastANI
[2024-01-25 17:53:09,426] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg27937e2e-09b3-4474-a9a2-1089da344901/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:53:09,426] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg27937e2e-09b3-4474-a9a2-1089da344901/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:53:09,432] [INFO] Found 8 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 17:53:09,432] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:53:09,432] [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 felsineum	strain=DSM 794	GCA_002006355.2	36839	36839	type	True	100.0	1741	1746	95	conclusive
Clostridium felsineum	strain=DSM 7320	GCA_002006215.2	36839	36839	type	True	98.1492	1522	1746	95	conclusive
Clostridium felsineum	strain=DSM 793	GCA_002006235.2	36839	36839	type	True	98.0483	1433	1746	95	conclusive
Clostridium acetobutylicum	strain=ATCC 824	GCA_000008765.1	1488	1488	type	True	82.9234	934	1746	95	below_threshold
Clostridium hydrogenum	strain=CUEA01	GCA_021432385.1	2855764	2855764	type	True	78.3128	384	1746	95	below_threshold
Clostridium septicum	strain=FDAARGOS_1551	GCA_020736665.1	1504	1504	type	True	76.9315	155	1746	95	below_threshold
Haloimpatiens massiliensis	strain=Mt13	GCA_900184255.1	1658110	1658110	type	True	76.6885	149	1746	95	below_threshold
Clostridium rectalis	strain=Marseille-P4200	GCA_900626095.1	2040295	2040295	type	True	76.1584	163	1746	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:53:09,436] [INFO] DFAST Taxonomy check result was written to GCF_002006355.2_ASM200635v2_genomic.fna/tc_result.tsv
[2024-01-25 17:53:09,437] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:53:09,437] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:53:09,437] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg27937e2e-09b3-4474-a9a2-1089da344901/dqc_reference/checkm_data
[2024-01-25 17:53:09,438] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:53:09,488] [INFO] Task started: CheckM
[2024-01-25 17:53:09,489] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002006355.2_ASM200635v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002006355.2_ASM200635v2_genomic.fna/checkm_input GCF_002006355.2_ASM200635v2_genomic.fna/checkm_result
[2024-01-25 17:53:35,899] [INFO] Task succeeded: CheckM
[2024-01-25 17:53:35,900] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:53:35,921] [INFO] ===== Completeness check finished =====
[2024-01-25 17:53:35,921] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:53:35,922] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002006355.2_ASM200635v2_genomic.fna/markers.fasta)
[2024-01-25 17:53:35,922] [INFO] Task started: Blastn
[2024-01-25 17:53:35,922] [INFO] Running command: blastn -query GCF_002006355.2_ASM200635v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg27937e2e-09b3-4474-a9a2-1089da344901/dqc_reference/reference_markers_gtdb.fasta -out GCF_002006355.2_ASM200635v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:53:36,703] [INFO] Task succeeded: Blastn
[2024-01-25 17:53:36,708] [INFO] Selected 22 target genomes.
[2024-01-25 17:53:36,708] [INFO] Target genome list was writen to GCF_002006355.2_ASM200635v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:53:36,747] [INFO] Task started: fastANI
[2024-01-25 17:53:36,747] [INFO] Running command: fastANI --query /var/lib/cwl/stg1e3efd02-11dd-4fa1-a187-8b667b917f0f/GCF_002006355.2_ASM200635v2_genomic.fna.gz --refList GCF_002006355.2_ASM200635v2_genomic.fna/target_genomes_gtdb.txt --output GCF_002006355.2_ASM200635v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:53:52,612] [INFO] Task succeeded: fastANI
[2024-01-25 17:53:52,623] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:53:52,624] [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_002006355.1	s__Clostridium_S felsineum	99.9602	1674	1746	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	conclusive
GCF_000008765.1	s__Clostridium_S acetobutylicum	82.9249	931	1746	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	-
GCF_001705235.1	s__Clostridium_S pasteurianum_A	80.031	698	1746	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_000968375.1	s__Clostridium_AM scatologenes	77.4587	252	1746	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AM	96.092	N/A	N/A	N/A	N/A	1	-
GCF_000389635.1	s__Clostridium_I pasteurianum_A	77.1832	203	1746	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_003614235.1	s__Clostridium_H haemolyticum	77.1682	149	1746	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_H	95.0	98.44	97.38	0.90	0.84	13	-
GCF_003606265.1	s__Clostridium septicum	76.9757	152	1746	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.65	99.48	0.94	0.92	5	-
GCF_900184255.1	s__Haloimpatiens massiliensis	76.5976	148	1746	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Haloimpatiens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001243045.1	s__Clostridium_F niameyense	76.5784	142	1746	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	99.56	99.11	0.96	0.92	3	-
GCF_012926525.1	s__Clostridium_AM sp012926525	76.5383	250	1746	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AM	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009696465.1	s__Inconstantimicrobium porci	76.2778	103	1746	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Inconstantimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011065935.1	s__Clostridium_AD estertheticum_A	76.1411	126	1746	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AD	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017873235.1	s__Clostridium moniliforme	76.0348	150	1746	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_000816675.1	s__Clostridium_J argentinense	76.0267	141	1746	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J	95.0	99.28	97.50	0.97	0.91	8	-
GCA_012519845.1	s__Clostridium sp012519845	75.8221	107	1746	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_900111985.1	s__Clostridium_Z frigidicarnis	75.7777	162	1746	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_Z	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017888565.1	s__Clostridium sp017888565	75.5795	157	1746	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002341865.1	s__Clostridium_J sp002341865	75.5103	148	1746	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	-
GCF_015686845.1	s__JADPRS01 sp015686845	75.1665	62	1746	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Thermotaleaceae;g__JADPRS01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:53:52,625] [INFO] GTDB search result was written to GCF_002006355.2_ASM200635v2_genomic.fna/result_gtdb.tsv
[2024-01-25 17:53:52,626] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:53:52,629] [INFO] DFAST_QC result json was written to GCF_002006355.2_ASM200635v2_genomic.fna/dqc_result.json
[2024-01-25 17:53:52,629] [INFO] DFAST_QC completed!
[2024-01-25 17:53:52,629] [INFO] Total running time: 0h1m2s