[2024-01-24 14:22:17,237] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:17,240] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:17,240] [INFO] DQC Reference Directory: /var/lib/cwl/stg691a091c-4da5-4e38-bb71-d75130cde0b6/dqc_reference
[2024-01-24 14:22:18,552] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:18,553] [INFO] Task started: Prodigal
[2024-01-24 14:22:18,553] [INFO] Running command: gunzip -c /var/lib/cwl/stgc5283cb4-c0e5-4787-9b59-f913df4badaa/GCF_014836835.1_ASM1483683v1_genomic.fna.gz | prodigal -d GCF_014836835.1_ASM1483683v1_genomic.fna/cds.fna -a GCF_014836835.1_ASM1483683v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:24,113] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:24,113] [INFO] Task started: HMMsearch
[2024-01-24 14:22:24,113] [INFO] Running command: hmmsearch --tblout GCF_014836835.1_ASM1483683v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg691a091c-4da5-4e38-bb71-d75130cde0b6/dqc_reference/reference_markers.hmm GCF_014836835.1_ASM1483683v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:24,406] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:24,407] [INFO] Found 6/6 markers.
[2024-01-24 14:22:24,442] [INFO] Query marker FASTA was written to GCF_014836835.1_ASM1483683v1_genomic.fna/markers.fasta
[2024-01-24 14:22:24,443] [INFO] Task started: Blastn
[2024-01-24 14:22:24,443] [INFO] Running command: blastn -query GCF_014836835.1_ASM1483683v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg691a091c-4da5-4e38-bb71-d75130cde0b6/dqc_reference/reference_markers.fasta -out GCF_014836835.1_ASM1483683v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:25,054] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:25,058] [INFO] Selected 22 target genomes.
[2024-01-24 14:22:25,059] [INFO] Target genome list was writen to GCF_014836835.1_ASM1483683v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:25,077] [INFO] Task started: fastANI
[2024-01-24 14:22:25,078] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5283cb4-c0e5-4787-9b59-f913df4badaa/GCF_014836835.1_ASM1483683v1_genomic.fna.gz --refList GCF_014836835.1_ASM1483683v1_genomic.fna/target_genomes.txt --output GCF_014836835.1_ASM1483683v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:39,747] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:39,748] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg691a091c-4da5-4e38-bb71-d75130cde0b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:39,748] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg691a091c-4da5-4e38-bb71-d75130cde0b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:39,767] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:22:39,767] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:39,768] [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 faecium	strain=N37	GCA_014836835.1	2762223	2762223	type	True	100.0	1185	1194	95	conclusive
Clostridium senegalense	strain=type strain: JC122	GCA_000285575.1	1465809	1465809	type	True	78.6943	350	1194	95	below_threshold
Clostridium ihumii	strain=AP5	GCA_000612845.1	1470356	1470356	type	True	78.1431	365	1194	95	below_threshold
Clostridium simiarum	strain=MSJ-4	GCA_018919175.1	2841506	2841506	type	True	77.9256	208	1194	95	below_threshold
Clostridium punense	strain=DSM 28650	GCA_017874425.1	1054297	1054297	type	True	77.4572	233	1194	95	below_threshold
Hathewaya histolytica	strain=NCTC503	GCA_901482605.1	1498	1498	type	True	77.2298	154	1194	95	below_threshold
Clostridium tetanomorphum	strain=DSM 4474	GCA_017873215.1	1553	1553	type	True	77.1311	218	1194	95	below_threshold
Haloimpatiens massiliensis	strain=Mt13	GCA_900184255.1	1658110	1658110	type	True	77.0096	199	1194	95	below_threshold
Clostridium lundense	strain=DSM 17049	GCA_000619945.1	319475	319475	type	True	76.9641	203	1194	95	below_threshold
Clostridium tagluense	strain=A121	GCA_003865095.1	360422	360422	type	True	76.7154	194	1194	95	below_threshold
Clostridium hydrogeniformans	strain=DSM 21757	GCA_000686705.1	349933	349933	type	True	76.6628	179	1194	95	below_threshold
Clostridium gallinarum	strain=Sa3CUN1	GCA_014836325.1	2762246	2762246	type	True	76.3839	140	1194	95	below_threshold
Clostridium massiliodielmoense	strain=MT26	GCA_900176615.1	1776385	1776385	type	True	76.3699	148	1194	95	below_threshold
Clostridium thermobutyricum	strain=DSM 4928	GCA_002050515.1	29372	29372	type	True	76.2484	183	1194	95	below_threshold
Clostridium autoethanogenum	strain=DSM 10061	GCA_000484505.2	84023	84023	suspected-type	True	76.2328	119	1194	95	below_threshold
Clostridium cavendishii	strain=DSM 21758	GCA_900141845.1	349931	349931	type	True	76.131	208	1194	95	below_threshold
Clostridium grantii	strain=DSM 8605	GCA_900129965.1	40575	40575	type	True	76.1239	122	1194	95	below_threshold
Clostridium hydrogenum	strain=CUEA01	GCA_021432385.1	2855764	2855764	type	True	75.9697	134	1194	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:39,770] [INFO] DFAST Taxonomy check result was written to GCF_014836835.1_ASM1483683v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:39,770] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:39,770] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:39,770] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg691a091c-4da5-4e38-bb71-d75130cde0b6/dqc_reference/checkm_data
[2024-01-24 14:22:39,772] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:39,813] [INFO] Task started: CheckM
[2024-01-24 14:22:39,813] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014836835.1_ASM1483683v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014836835.1_ASM1483683v1_genomic.fna/checkm_input GCF_014836835.1_ASM1483683v1_genomic.fna/checkm_result
[2024-01-24 14:23:02,977] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:02,978] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:03,001] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:03,002] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:03,002] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014836835.1_ASM1483683v1_genomic.fna/markers.fasta)
[2024-01-24 14:23:03,002] [INFO] Task started: Blastn
[2024-01-24 14:23:03,003] [INFO] Running command: blastn -query GCF_014836835.1_ASM1483683v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg691a091c-4da5-4e38-bb71-d75130cde0b6/dqc_reference/reference_markers_gtdb.fasta -out GCF_014836835.1_ASM1483683v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:03,780] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:03,784] [INFO] Selected 11 target genomes.
[2024-01-24 14:23:03,784] [INFO] Target genome list was writen to GCF_014836835.1_ASM1483683v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:03,794] [INFO] Task started: fastANI
[2024-01-24 14:23:03,795] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5283cb4-c0e5-4787-9b59-f913df4badaa/GCF_014836835.1_ASM1483683v1_genomic.fna.gz --refList GCF_014836835.1_ASM1483683v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014836835.1_ASM1483683v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:12,607] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:12,616] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:12,616] [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_014836835.1	s__Clostridium_J sp900547625	100.0	1185	1194	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J	95.0	99.59	99.59	0.89	0.87	3	conclusive
GCF_000816675.1	s__Clostridium_J argentinense	87.5473	968	1194	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_002341865.1	s__Clostridium_J sp002341865	87.3328	926	1194	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	-
GCA_002455975.1	s__Clostridium_J sp002455975	87.2379	908	1194	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_000285575.1	s__Clostridium_J senegalense	78.7184	348	1194	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	-
GCF_000612845.1	s__Clostridium_J ihumii	78.1394	366	1194	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J	95.0	100.00	100.00	0.99	0.99	2	-
GCF_002008345.1	s__Clostridium_F tepidum	77.8087	234	1194	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	99.70	99.54	0.93	0.92	5	-
GCF_000300195.1	s__Clostridium_J tunisiense	77.4691	227	1194	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J	95.0	96.47	95.03	0.88	0.88	3	-
GCF_001405015.1	s__Clostridium disporicum	76.3232	141	1194	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.24	98.87	0.93	0.88	4	-
GCF_002050515.1	s__Clostridium thermobutyricum	76.2494	181	1194	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	97.10	97.10	0.91	0.89	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:23:12,619] [INFO] GTDB search result was written to GCF_014836835.1_ASM1483683v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:12,619] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:12,625] [INFO] DFAST_QC result json was written to GCF_014836835.1_ASM1483683v1_genomic.fna/dqc_result.json
[2024-01-24 14:23:12,625] [INFO] DFAST_QC completed!
[2024-01-24 14:23:12,625] [INFO] Total running time: 0h0m55s