[2024-01-24 15:19:04,609] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:19:04,612] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:19:04,612] [INFO] DQC Reference Directory: /var/lib/cwl/stgeee638d4-e98b-471f-bc3f-c996c04632a6/dqc_reference
[2024-01-24 15:19:05,835] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:19:05,836] [INFO] Task started: Prodigal
[2024-01-24 15:19:05,836] [INFO] Running command: gunzip -c /var/lib/cwl/stg926d6a27-303e-44e4-b92f-ec0e45d4a57c/GCF_003313305.1_ASM331330v1_genomic.fna.gz | prodigal -d GCF_003313305.1_ASM331330v1_genomic.fna/cds.fna -a GCF_003313305.1_ASM331330v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:19:17,534] [INFO] Task succeeded: Prodigal
[2024-01-24 15:19:17,535] [INFO] Task started: HMMsearch
[2024-01-24 15:19:17,535] [INFO] Running command: hmmsearch --tblout GCF_003313305.1_ASM331330v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeee638d4-e98b-471f-bc3f-c996c04632a6/dqc_reference/reference_markers.hmm GCF_003313305.1_ASM331330v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:19:17,865] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:19:17,866] [INFO] Found 6/6 markers.
[2024-01-24 15:19:17,930] [INFO] Query marker FASTA was written to GCF_003313305.1_ASM331330v1_genomic.fna/markers.fasta
[2024-01-24 15:19:17,930] [INFO] Task started: Blastn
[2024-01-24 15:19:17,931] [INFO] Running command: blastn -query GCF_003313305.1_ASM331330v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeee638d4-e98b-471f-bc3f-c996c04632a6/dqc_reference/reference_markers.fasta -out GCF_003313305.1_ASM331330v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:18,602] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:18,606] [INFO] Selected 29 target genomes.
[2024-01-24 15:19:18,606] [INFO] Target genome list was writen to GCF_003313305.1_ASM331330v1_genomic.fna/target_genomes.txt
[2024-01-24 15:19:18,630] [INFO] Task started: fastANI
[2024-01-24 15:19:18,631] [INFO] Running command: fastANI --query /var/lib/cwl/stg926d6a27-303e-44e4-b92f-ec0e45d4a57c/GCF_003313305.1_ASM331330v1_genomic.fna.gz --refList GCF_003313305.1_ASM331330v1_genomic.fna/target_genomes.txt --output GCF_003313305.1_ASM331330v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:36,568] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:36,569] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeee638d4-e98b-471f-bc3f-c996c04632a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:36,569] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeee638d4-e98b-471f-bc3f-c996c04632a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:36,583] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:19:36,584] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:36,584] [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
Vallitalea guaymasensis	strain=Ra1766G1	GCA_018141425.1	1185412	1185412	type	True	97.323	1652	2137	95	conclusive
Vallitalea pronyensis	strain=FatNI3	GCA_018141445.1	1348613	1348613	type	True	77.7995	288	2137	95	below_threshold
Crassaminicella profunda	strain=Ra1766H	GCA_019884785.1	1286698	1286698	type	True	76.8204	83	2137	95	below_threshold
Natranaerovirga hydrolytica	strain=DSM 24176	GCA_004339095.1	680378	680378	type	True	76.4931	79	2137	95	below_threshold
Natranaerovirga pectinivora	strain=DSM 24629	GCA_004342165.1	682400	682400	type	True	76.4732	88	2137	95	below_threshold
Clostridium fallax	strain=NCTC8380	GCA_900461065.1	1533	1533	type	True	76.4698	79	2137	95	below_threshold
Clostridium cellulovorans	strain=743B	GCA_000145275.1	1493	1493	type	True	75.9455	81	2137	95	below_threshold
Caminicella sporogenes	strain=DSM 14501	GCA_900142285.1	166485	166485	type	True	75.2767	51	2137	95	below_threshold
Clostridium collagenovorans	strain=DSM 3089	GCA_900130005.1	29357	29357	type	True	75.1016	56	2137	95	below_threshold
Anaeromonas gelatinilytica	strain=D2Q-14	GCA_016820635.1	2683194	2683194	type	True	75.0867	59	2137	95	below_threshold
Clostridium chromiireducens	strain=DSM 23318	GCA_002029255.1	225345	225345	type	True	75.0219	86	2137	95	below_threshold
Clostridium acetireducens	strain=DSM 10703	GCA_001758365.1	76489	76489	type	True	74.8895	69	2137	95	below_threshold
Clostridium tarantellae	strain=DSM 3997	GCA_009295725.1	39493	39493	type	True	74.7589	87	2137	95	below_threshold
Clostridium arbusti	strain=SL206	GCA_000246895.2	1137848	1137848	type	True	74.6251	53	2137	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:36,586] [INFO] DFAST Taxonomy check result was written to GCF_003313305.1_ASM331330v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:36,586] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:36,586] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:36,586] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeee638d4-e98b-471f-bc3f-c996c04632a6/dqc_reference/checkm_data
[2024-01-24 15:19:36,588] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:36,647] [INFO] Task started: CheckM
[2024-01-24 15:19:36,648] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003313305.1_ASM331330v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003313305.1_ASM331330v1_genomic.fna/checkm_input GCF_003313305.1_ASM331330v1_genomic.fna/checkm_result
[2024-01-24 15:20:15,857] [INFO] Task succeeded: CheckM
[2024-01-24 15:20:15,859] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:20:15,882] [INFO] ===== Completeness check finished =====
[2024-01-24 15:20:15,882] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:20:15,883] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003313305.1_ASM331330v1_genomic.fna/markers.fasta)
[2024-01-24 15:20:15,883] [INFO] Task started: Blastn
[2024-01-24 15:20:15,883] [INFO] Running command: blastn -query GCF_003313305.1_ASM331330v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeee638d4-e98b-471f-bc3f-c996c04632a6/dqc_reference/reference_markers_gtdb.fasta -out GCF_003313305.1_ASM331330v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:20:16,879] [INFO] Task succeeded: Blastn
[2024-01-24 15:20:16,883] [INFO] Selected 28 target genomes.
[2024-01-24 15:20:16,883] [INFO] Target genome list was writen to GCF_003313305.1_ASM331330v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:20:16,919] [INFO] Task started: fastANI
[2024-01-24 15:20:16,919] [INFO] Running command: fastANI --query /var/lib/cwl/stg926d6a27-303e-44e4-b92f-ec0e45d4a57c/GCF_003313305.1_ASM331330v1_genomic.fna.gz --refList GCF_003313305.1_ASM331330v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003313305.1_ASM331330v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:20:33,842] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:33,855] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:20:33,856] [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_018141425.1	s__Vallitalea guaymasensis	97.3144	1653	2137	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Vallitaleaceae;g__Vallitalea	95.0	97.34	97.34	0.88	0.88	2	conclusive
GCF_018141445.1	s__Vallitalea pronyensis	77.8228	289	2137	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Vallitaleaceae;g__Vallitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342165.1	s__Natranaerovirga pectinivora	76.4938	87	2137	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__DSM-24629;g__Natranaerovirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339095.1	s__Natranaerovirga hydrolytica	76.4931	79	2137	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__DSM-24629;g__Natranaerovirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015057455.1	s__SIG301 sp015057455	75.6077	56	2137	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__SIG301	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018918325.1	s__Clostridium sp018918325	75.2889	54	2137	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_902362365.1	s__GCA-900066495 sp902362365	75.2118	70	2137	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__GCA-900066495	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900130005.1	s__Clostridium_D collagenovorans	75.0057	56	2137	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001758365.1	s__Clostridium_C acetireducens	74.8994	67	2137	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_009295725.1	s__Clostridium_P tarantellae	74.7547	88	2137	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	-
--------------------------------------------------------------------------------
[2024-01-24 15:20:33,857] [INFO] GTDB search result was written to GCF_003313305.1_ASM331330v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:20:33,858] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:20:33,861] [INFO] DFAST_QC result json was written to GCF_003313305.1_ASM331330v1_genomic.fna/dqc_result.json
[2024-01-24 15:20:33,861] [INFO] DFAST_QC completed!
[2024-01-24 15:20:33,861] [INFO] Total running time: 0h1m29s