[2024-01-24 13:57:43,853] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:43,855] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:43,855] [INFO] DQC Reference Directory: /var/lib/cwl/stge816afaf-5483-411a-9703-ca1c7d243628/dqc_reference
[2024-01-24 13:57:45,115] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:45,116] [INFO] Task started: Prodigal
[2024-01-24 13:57:45,116] [INFO] Running command: gunzip -c /var/lib/cwl/stgff089c3f-3ab1-4ac3-bfeb-39942194df84/GCF_018861865.1_ASM1886186v1_genomic.fna.gz | prodigal -d GCF_018861865.1_ASM1886186v1_genomic.fna/cds.fna -a GCF_018861865.1_ASM1886186v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:51,443] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:51,443] [INFO] Task started: HMMsearch
[2024-01-24 13:57:51,443] [INFO] Running command: hmmsearch --tblout GCF_018861865.1_ASM1886186v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge816afaf-5483-411a-9703-ca1c7d243628/dqc_reference/reference_markers.hmm GCF_018861865.1_ASM1886186v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:51,724] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:51,725] [INFO] Found 6/6 markers.
[2024-01-24 13:57:51,757] [INFO] Query marker FASTA was written to GCF_018861865.1_ASM1886186v1_genomic.fna/markers.fasta
[2024-01-24 13:57:51,757] [INFO] Task started: Blastn
[2024-01-24 13:57:51,757] [INFO] Running command: blastn -query GCF_018861865.1_ASM1886186v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge816afaf-5483-411a-9703-ca1c7d243628/dqc_reference/reference_markers.fasta -out GCF_018861865.1_ASM1886186v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:52,339] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:52,343] [INFO] Selected 12 target genomes.
[2024-01-24 13:57:52,343] [INFO] Target genome list was writen to GCF_018861865.1_ASM1886186v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:52,465] [INFO] Task started: fastANI
[2024-01-24 13:57:52,465] [INFO] Running command: fastANI --query /var/lib/cwl/stgff089c3f-3ab1-4ac3-bfeb-39942194df84/GCF_018861865.1_ASM1886186v1_genomic.fna.gz --refList GCF_018861865.1_ASM1886186v1_genomic.fna/target_genomes.txt --output GCF_018861865.1_ASM1886186v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:03,481] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:03,482] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge816afaf-5483-411a-9703-ca1c7d243628/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:03,482] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge816afaf-5483-411a-9703-ca1c7d243628/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:03,492] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:03,492] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:03,493] [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 frigoris	strain=DSM 14204	GCA_018861865.1	205327	205327	type	True	100.0	1292	1301	95	conclusive
Clostridium estertheticum subsp. estertheticum	strain=DSM 8809	GCA_001877035.1	1552	238834	type	True	89.5739	984	1301	95	below_threshold
Clostridium estertheticum subsp. laramiense	strain=DSM 14864	GCA_008933175.2	205326	238834	type	True	89.5276	996	1301	95	below_threshold
Clostridium psychrophilum	strain=DSM 14207	GCA_018861705.1	132926	132926	type	True	83.1602	790	1301	95	below_threshold
Clostridium algoriphilum	strain=DSM 16153	GCA_020443705.1	198347	198347	type	True	82.7813	781	1301	95	below_threshold
Clostridium lacusfryxellense	strain=DSM 14205	GCA_018861735.1	205328	205328	type	True	81.8002	781	1301	95	below_threshold
Clostridium tagluense	strain=A121	GCA_003865095.1	360422	360422	type	True	81.3215	674	1301	95	below_threshold
Clostridium oryzae	strain=DSM 28571	GCA_002029235.1	1450648	1450648	type	True	76.2469	81	1301	95	below_threshold
Clostridium grantii	strain=DSM 8605	GCA_900129965.1	40575	40575	type	True	76.0486	130	1301	95	below_threshold
Clostridium swellfunianum	strain=CICC 10730	GCA_023656515.1	1367462	1367462	type	True	76.0242	77	1301	95	below_threshold
Crassaminicella profunda	strain=Ra1766H	GCA_019884785.1	1286698	1286698	type	True	75.0741	61	1301	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:03,494] [INFO] DFAST Taxonomy check result was written to GCF_018861865.1_ASM1886186v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:03,495] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:03,495] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:03,495] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge816afaf-5483-411a-9703-ca1c7d243628/dqc_reference/checkm_data
[2024-01-24 13:58:03,496] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:03,540] [INFO] Task started: CheckM
[2024-01-24 13:58:03,540] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018861865.1_ASM1886186v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018861865.1_ASM1886186v1_genomic.fna/checkm_input GCF_018861865.1_ASM1886186v1_genomic.fna/checkm_result
[2024-01-24 13:58:29,928] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:29,932] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:29,953] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:29,953] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:29,953] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018861865.1_ASM1886186v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:29,954] [INFO] Task started: Blastn
[2024-01-24 13:58:29,954] [INFO] Running command: blastn -query GCF_018861865.1_ASM1886186v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge816afaf-5483-411a-9703-ca1c7d243628/dqc_reference/reference_markers_gtdb.fasta -out GCF_018861865.1_ASM1886186v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:30,790] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:30,793] [INFO] Selected 7 target genomes.
[2024-01-24 13:58:30,793] [INFO] Target genome list was writen to GCF_018861865.1_ASM1886186v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:30,824] [INFO] Task started: fastANI
[2024-01-24 13:58:30,824] [INFO] Running command: fastANI --query /var/lib/cwl/stgff089c3f-3ab1-4ac3-bfeb-39942194df84/GCF_018861865.1_ASM1886186v1_genomic.fna.gz --refList GCF_018861865.1_ASM1886186v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018861865.1_ASM1886186v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:39,173] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:39,182] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:39,182] [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_018861865.1	s__Clostridium_AD frigoris	100.0	1292	1301	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	conclusive
GCF_018861325.1	s__Clostridium_AD estertheticum_C	89.9012	992	1301	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AD	95.0	97.28	95.54	0.84	0.79	3	-
GCF_018861905.1	s__Clostridium_AD sp018861905	89.8714	1000	1301	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_001877035.1	s__Clostridium_AD estertheticum	89.5738	985	1301	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AD	95.0	98.08	95.13	0.86	0.81	10	-
GCF_018861705.1	s__Clostridium_AD psychrophilum	83.1794	788	1301	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	-
GCA_002403785.1	s__Clostridium_AD sp002403785	82.8929	715	1301	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_011065905.1	s__Clostridium_AD estertheticum_B	82.5177	648	1301	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AD	95.0	97.19	97.19	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:39,184] [INFO] GTDB search result was written to GCF_018861865.1_ASM1886186v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:39,184] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:39,191] [INFO] DFAST_QC result json was written to GCF_018861865.1_ASM1886186v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:39,192] [INFO] DFAST_QC completed!
[2024-01-24 13:58:39,192] [INFO] Total running time: 0h0m55s