[2024-01-25 19:02:20,501] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:02:20,502] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:02:20,502] [INFO] DQC Reference Directory: /var/lib/cwl/stgc5caae03-3f55-4d93-bf5f-4c257bbeaf6e/dqc_reference
[2024-01-25 19:02:21,654] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:02:21,654] [INFO] Task started: Prodigal
[2024-01-25 19:02:21,654] [INFO] Running command: gunzip -c /var/lib/cwl/stg60ceb8fc-3289-47bb-bccc-b0c75779de76/GCF_017874415.1_ASM1787441v1_genomic.fna.gz | prodigal -d GCF_017874415.1_ASM1787441v1_genomic.fna/cds.fna -a GCF_017874415.1_ASM1787441v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:02:25,981] [INFO] Task succeeded: Prodigal
[2024-01-25 19:02:25,981] [INFO] Task started: HMMsearch
[2024-01-25 19:02:25,981] [INFO] Running command: hmmsearch --tblout GCF_017874415.1_ASM1787441v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc5caae03-3f55-4d93-bf5f-4c257bbeaf6e/dqc_reference/reference_markers.hmm GCF_017874415.1_ASM1787441v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:02:26,249] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:02:26,250] [INFO] Found 6/6 markers.
[2024-01-25 19:02:26,277] [INFO] Query marker FASTA was written to GCF_017874415.1_ASM1787441v1_genomic.fna/markers.fasta
[2024-01-25 19:02:26,277] [INFO] Task started: Blastn
[2024-01-25 19:02:26,277] [INFO] Running command: blastn -query GCF_017874415.1_ASM1787441v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5caae03-3f55-4d93-bf5f-4c257bbeaf6e/dqc_reference/reference_markers.fasta -out GCF_017874415.1_ASM1787441v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:02:26,835] [INFO] Task succeeded: Blastn
[2024-01-25 19:02:26,837] [INFO] Selected 18 target genomes.
[2024-01-25 19:02:26,838] [INFO] Target genome list was writen to GCF_017874415.1_ASM1787441v1_genomic.fna/target_genomes.txt
[2024-01-25 19:02:26,858] [INFO] Task started: fastANI
[2024-01-25 19:02:26,859] [INFO] Running command: fastANI --query /var/lib/cwl/stg60ceb8fc-3289-47bb-bccc-b0c75779de76/GCF_017874415.1_ASM1787441v1_genomic.fna.gz --refList GCF_017874415.1_ASM1787441v1_genomic.fna/target_genomes.txt --output GCF_017874415.1_ASM1787441v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:02:38,165] [INFO] Task succeeded: fastANI
[2024-01-25 19:02:38,165] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc5caae03-3f55-4d93-bf5f-4c257bbeaf6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:02:38,166] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc5caae03-3f55-4d93-bf5f-4c257bbeaf6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:02:38,175] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:02:38,176] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:02:38,176] [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 algifaecis	strain=DSM 28783	GCA_017874415.1	1472040	1472040	type	True	100.0	957	960	95	conclusive
Clostridium tyrobutyricum	strain=DSM 2637	GCA_000429805.1	1519	1519	type	True	79.2804	424	960	95	below_threshold
Clostridium tyrobutyricum	strain=ATCC 25755	GCA_000359585.1	1519	1519	type	True	79.2013	415	960	95	below_threshold
Clostridium tyrobutyricum	strain=DSM 2637	GCA_000392375.2	1519	1519	type	True	79.1623	404	960	95	below_threshold
Clostridium ljungdahlii	strain=DSM 13528	GCA_000143685.1	1538	1538	suspected-type	True	78.9607	365	960	95	below_threshold
Clostridium autoethanogenum	strain=DSM 10061	GCA_000484505.2	84023	84023	suspected-type	True	78.9213	355	960	95	below_threshold
Clostridium autoethanogenum	strain=DSM 10061	GCA_000427255.1	84023	84023	suspected-type	True	78.9063	344	960	95	below_threshold
Clostridium autoethanogenum	strain=JA1-1	GCA_002189005.1	84023	84023	suspected-type	True	78.8705	353	960	95	below_threshold
Clostridium carboxidivorans	strain=P7	GCA_001038625.1	217159	217159	type	True	77.8273	264	960	95	below_threshold
Clostridium kluyveri	strain=NBRC 12016	GCA_000010265.1	1534	1534	type	True	77.4931	264	960	95	below_threshold
Clostridium kluyveri	strain=DSM 555	GCA_000016505.1	1534	1534	type	True	77.4911	264	960	95	below_threshold
Clostridium thailandense	strain=PL3	GCA_019207025.1	2794346	2794346	type	True	76.8948	214	960	95	below_threshold
Clostridium cagae	strain=Marseille-P4344	GCA_900290265.1	2080751	2080751	type	True	76.1803	107	960	95	below_threshold
Clostridium uliginosum	strain=DSM 12992	GCA_900112485.1	119641	119641	type	True	76.0488	119	960	95	below_threshold
Clostridium cibarium	strain=Sa3CVN1	GCA_014836335.1	2762247	2762247	type	True	75.967	88	960	95	below_threshold
Clostridium moniliforme	strain=DSM 3984	GCA_017873235.1	39489	39489	type	True	75.5397	97	960	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:02:38,177] [INFO] DFAST Taxonomy check result was written to GCF_017874415.1_ASM1787441v1_genomic.fna/tc_result.tsv
[2024-01-25 19:02:38,178] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:02:38,178] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:02:38,178] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc5caae03-3f55-4d93-bf5f-4c257bbeaf6e/dqc_reference/checkm_data
[2024-01-25 19:02:38,179] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:02:38,208] [INFO] Task started: CheckM
[2024-01-25 19:02:38,209] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017874415.1_ASM1787441v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017874415.1_ASM1787441v1_genomic.fna/checkm_input GCF_017874415.1_ASM1787441v1_genomic.fna/checkm_result
[2024-01-25 19:02:56,926] [INFO] Task succeeded: CheckM
[2024-01-25 19:02:56,927] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:02:56,946] [INFO] ===== Completeness check finished =====
[2024-01-25 19:02:56,946] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:02:56,947] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017874415.1_ASM1787441v1_genomic.fna/markers.fasta)
[2024-01-25 19:02:56,947] [INFO] Task started: Blastn
[2024-01-25 19:02:56,947] [INFO] Running command: blastn -query GCF_017874415.1_ASM1787441v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5caae03-3f55-4d93-bf5f-4c257bbeaf6e/dqc_reference/reference_markers_gtdb.fasta -out GCF_017874415.1_ASM1787441v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:02:57,724] [INFO] Task succeeded: Blastn
[2024-01-25 19:02:57,727] [INFO] Selected 18 target genomes.
[2024-01-25 19:02:57,727] [INFO] Target genome list was writen to GCF_017874415.1_ASM1787441v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:02:57,744] [INFO] Task started: fastANI
[2024-01-25 19:02:57,744] [INFO] Running command: fastANI --query /var/lib/cwl/stg60ceb8fc-3289-47bb-bccc-b0c75779de76/GCF_017874415.1_ASM1787441v1_genomic.fna.gz --refList GCF_017874415.1_ASM1787441v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017874415.1_ASM1787441v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:03:09,380] [INFO] Task succeeded: fastANI
[2024-01-25 19:03:09,390] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:03:09,391] [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_017874415.1	s__Clostridium_B algifaecis	100.0	957	960	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	conclusive
GCF_000359585.1	s__Clostridium_B tyrobutyricum	79.1954	416	960	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_B	95.0	99.17	95.02	0.91	0.82	32	-
GCF_014050525.1	s__Clostridium_B sp014050525	79.1584	361	960	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_001675165.1	s__Clostridium_B ragsdalei	78.9812	333	960	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_B	95.0	98.18	98.18	0.88	0.88	2	-
GCF_001636845.1	s__Clostridium_B ljungdahlii_A	78.9752	358	960	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_000143685.1	s__Clostridium_B ljungdahlii	78.9615	364	960	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_B	95.0	98.76	97.79	0.92	0.88	9	-
GCF_004006395.2	s__Clostridium_B sp004006395	78.7155	347	960	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_001038625.1	s__Clostridium_AM carboxidivorans	77.8273	264	960	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AM	95.0	99.97	99.96	1.00	0.99	3	-
GCF_000016505.1	s__Clostridium_B kluyveri	77.4812	265	960	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_B	95.0	97.52	95.05	0.91	0.81	3	-
GCF_000968375.1	s__Clostridium_AM scatologenes	77.4221	284	960	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	-
GCA_902809985.1	s__Clostridium_B sp902809985	77.2258	219	960	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_B	95.0	99.08	99.06	0.93	0.92	3	-
GCF_000807255.1	s__Clostridium_I pasteurianum	76.8507	158	960	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_I	95.0	99.98	99.90	1.00	0.99	7	-
GCF_900626095.1	s__Clostridium_AS rectalis	76.6206	117	960	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AS	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001276215.1	s__Clostridium_F sp001276215	76.3284	137	960	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	97.32	95.44	0.88	0.82	10	-
GCF_007115085.1	s__Clostridium sp007115085	76.1091	83	960	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.42	99.42	0.90	0.90	2	-
GCA_016650035.1	s__Clostridium_AD sp016650035	75.9644	78	960	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_018917145.1	s__Clostridium_AN bornimense_A	75.4168	85	960	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AN	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000789395.1	s__Clostridium baratii	75.4034	103	960	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	96.53	95.37	0.92	0.89	15	-
--------------------------------------------------------------------------------
[2024-01-25 19:03:09,392] [INFO] GTDB search result was written to GCF_017874415.1_ASM1787441v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:03:09,392] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:03:09,395] [INFO] DFAST_QC result json was written to GCF_017874415.1_ASM1787441v1_genomic.fna/dqc_result.json
[2024-01-25 19:03:09,395] [INFO] DFAST_QC completed!
[2024-01-25 19:03:09,396] [INFO] Total running time: 0h0m49s