[2024-01-25 18:39:35,931] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:39:35,933] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:39:35,933] [INFO] DQC Reference Directory: /var/lib/cwl/stg8a470ec5-0be7-44ff-9441-3c4a7b2b073c/dqc_reference
[2024-01-25 18:39:37,080] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:39:37,080] [INFO] Task started: Prodigal
[2024-01-25 18:39:37,081] [INFO] Running command: gunzip -c /var/lib/cwl/stg4011a6df-fd89-4207-b77a-9bb3121ea796/GCF_011017965.1_ASM1101796v1_genomic.fna.gz | prodigal -d GCF_011017965.1_ASM1101796v1_genomic.fna/cds.fna -a GCF_011017965.1_ASM1101796v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:39:42,043] [INFO] Task succeeded: Prodigal
[2024-01-25 18:39:42,043] [INFO] Task started: HMMsearch
[2024-01-25 18:39:42,044] [INFO] Running command: hmmsearch --tblout GCF_011017965.1_ASM1101796v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8a470ec5-0be7-44ff-9441-3c4a7b2b073c/dqc_reference/reference_markers.hmm GCF_011017965.1_ASM1101796v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:39:42,311] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:39:42,312] [INFO] Found 6/6 markers.
[2024-01-25 18:39:42,345] [INFO] Query marker FASTA was written to GCF_011017965.1_ASM1101796v1_genomic.fna/markers.fasta
[2024-01-25 18:39:42,345] [INFO] Task started: Blastn
[2024-01-25 18:39:42,345] [INFO] Running command: blastn -query GCF_011017965.1_ASM1101796v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a470ec5-0be7-44ff-9441-3c4a7b2b073c/dqc_reference/reference_markers.fasta -out GCF_011017965.1_ASM1101796v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:39:42,910] [INFO] Task succeeded: Blastn
[2024-01-25 18:39:42,912] [INFO] Selected 16 target genomes.
[2024-01-25 18:39:42,913] [INFO] Target genome list was writen to GCF_011017965.1_ASM1101796v1_genomic.fna/target_genomes.txt
[2024-01-25 18:39:42,918] [INFO] Task started: fastANI
[2024-01-25 18:39:42,918] [INFO] Running command: fastANI --query /var/lib/cwl/stg4011a6df-fd89-4207-b77a-9bb3121ea796/GCF_011017965.1_ASM1101796v1_genomic.fna.gz --refList GCF_011017965.1_ASM1101796v1_genomic.fna/target_genomes.txt --output GCF_011017965.1_ASM1101796v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:39:56,276] [INFO] Task succeeded: fastANI
[2024-01-25 18:39:56,276] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8a470ec5-0be7-44ff-9441-3c4a7b2b073c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:39:56,276] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8a470ec5-0be7-44ff-9441-3c4a7b2b073c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:39:56,286] [INFO] Found 16 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 18:39:56,286] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 18:39:56,287] [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 botulinum	strain=ATCC 25763	GCA_011017965.1	1491	1491	type	True	100.0	1255	1259	95	inconclusive
Clostridium botulinum	strain=ATCC 25763	GCA_001276985.1	1491	1491	type	True	99.9951	1257	1259	95	inconclusive
Clostridium combesii	strain=DSM 20696	GCA_002749945.1	39481	39481	type	True	97.3249	1144	1259	95	inconclusive
Clostridium sporogenes	strain=NCTC13020	GCA_900461305.1	1509	1509	type	True	92.0334	1063	1259	95	below_threshold
Clostridium sporogenes	strain=DSM 795	GCA_001020205.1	1509	1509	type	True	92.0267	1059	1259	95	below_threshold
Clostridium sporogenes	strain=NCIMB 10696	GCA_000973705.1	1509	1509	type	True	92.0047	1058	1259	95	below_threshold
Clostridium simiarum	strain=MSJ-4	GCA_018919175.1	2841506	2841506	type	True	77.6932	236	1259	95	below_threshold
Clostridium muellerianum	strain=P21	GCA_012926525.1	2716538	2716538	type	True	77.1363	316	1259	95	below_threshold
Clostridium autoethanogenum	strain=DSM 10061	GCA_000484505.2	84023	84023	suspected-type	True	76.6265	182	1259	95	below_threshold
Clostridium bornimense	strain=type strain: M2/40	GCA_000577895.1	1216932	1216932	type	True	76.313	135	1259	95	below_threshold
Tissierella simiarum	strain=MSJ-40	GCA_018917865.1	2841534	2841534	type	True	76.2672	103	1259	95	below_threshold
Clostridium acidisoli	strain=DSM 12555	GCA_900176305.1	91624	91624	type	True	76.1817	160	1259	95	below_threshold
Clostridium swellfunianum	strain=CICC 10730	GCA_023656515.1	1367462	1367462	type	True	76.0757	108	1259	95	below_threshold
Clostridium kluyveri	strain=NBRC 12016	GCA_000010265.1	1534	1534	type	True	75.9123	182	1259	95	below_threshold
Clostridium kluyveri	strain=DSM 555	GCA_000016505.1	1534	1534	type	True	75.9118	182	1259	95	below_threshold
Clostridium chrysemydis	strain=PT	GCA_015234215.1	2665504	2665504	type	True	75.5238	155	1259	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:39:56,288] [INFO] DFAST Taxonomy check result was written to GCF_011017965.1_ASM1101796v1_genomic.fna/tc_result.tsv
[2024-01-25 18:39:56,288] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:39:56,289] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:39:56,289] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8a470ec5-0be7-44ff-9441-3c4a7b2b073c/dqc_reference/checkm_data
[2024-01-25 18:39:56,290] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:39:56,330] [INFO] Task started: CheckM
[2024-01-25 18:39:56,331] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011017965.1_ASM1101796v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011017965.1_ASM1101796v1_genomic.fna/checkm_input GCF_011017965.1_ASM1101796v1_genomic.fna/checkm_result
[2024-01-25 18:40:16,531] [INFO] Task succeeded: CheckM
[2024-01-25 18:40:16,532] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:40:16,551] [INFO] ===== Completeness check finished =====
[2024-01-25 18:40:16,552] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:40:16,553] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011017965.1_ASM1101796v1_genomic.fna/markers.fasta)
[2024-01-25 18:40:16,553] [INFO] Task started: Blastn
[2024-01-25 18:40:16,553] [INFO] Running command: blastn -query GCF_011017965.1_ASM1101796v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a470ec5-0be7-44ff-9441-3c4a7b2b073c/dqc_reference/reference_markers_gtdb.fasta -out GCF_011017965.1_ASM1101796v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:40:17,297] [INFO] Task succeeded: Blastn
[2024-01-25 18:40:17,300] [INFO] Selected 5 target genomes.
[2024-01-25 18:40:17,300] [INFO] Target genome list was writen to GCF_011017965.1_ASM1101796v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:40:17,303] [INFO] Task started: fastANI
[2024-01-25 18:40:17,303] [INFO] Running command: fastANI --query /var/lib/cwl/stg4011a6df-fd89-4207-b77a-9bb3121ea796/GCF_011017965.1_ASM1101796v1_genomic.fna.gz --refList GCF_011017965.1_ASM1101796v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011017965.1_ASM1101796v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:40:23,585] [INFO] Task succeeded: fastANI
[2024-01-25 18:40:23,589] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:40:23,590] [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_001276985.1	s__Clostridium_F botulinum	99.9951	1257	1259	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	97.69	95.97	0.92	0.83	213	conclusive
GCF_001889325.1	s__Clostridium_F botulinum_A	93.5751	1109	1259	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	95.92	95.51	0.89	0.85	52	-
GCF_001020205.1	s__Clostridium_F sporogenes	92.0209	1060	1259	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	99.24	98.80	0.94	0.88	81	-
GCF_001276215.1	s__Clostridium_F sp001276215	89.2704	954	1259	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_002008345.1	s__Clostridium_F tepidum	87.9452	795	1259	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	-
--------------------------------------------------------------------------------
[2024-01-25 18:40:23,597] [INFO] GTDB search result was written to GCF_011017965.1_ASM1101796v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:40:23,599] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:40:23,602] [INFO] DFAST_QC result json was written to GCF_011017965.1_ASM1101796v1_genomic.fna/dqc_result.json
[2024-01-25 18:40:23,602] [INFO] DFAST_QC completed!
[2024-01-25 18:40:23,602] [INFO] Total running time: 0h0m48s