[2024-01-24 12:43:54,222] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:43:54,225] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:43:54,225] [INFO] DQC Reference Directory: /var/lib/cwl/stg5d5e9257-1041-4a67-8b71-5a914dcb0831/dqc_reference
[2024-01-24 12:43:59,335] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:43:59,336] [INFO] Task started: Prodigal
[2024-01-24 12:43:59,337] [INFO] Running command: gunzip -c /var/lib/cwl/stge08b88bf-9c26-4ba6-b2c3-099862332544/GCF_002995845.1_ASM299584v1_genomic.fna.gz | prodigal -d GCF_002995845.1_ASM299584v1_genomic.fna/cds.fna -a GCF_002995845.1_ASM299584v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:06,585] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:06,586] [INFO] Task started: HMMsearch
[2024-01-24 12:44:06,586] [INFO] Running command: hmmsearch --tblout GCF_002995845.1_ASM299584v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5d5e9257-1041-4a67-8b71-5a914dcb0831/dqc_reference/reference_markers.hmm GCF_002995845.1_ASM299584v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:06,875] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:06,877] [INFO] Found 6/6 markers.
[2024-01-24 12:44:06,910] [INFO] Query marker FASTA was written to GCF_002995845.1_ASM299584v1_genomic.fna/markers.fasta
[2024-01-24 12:44:06,911] [INFO] Task started: Blastn
[2024-01-24 12:44:06,911] [INFO] Running command: blastn -query GCF_002995845.1_ASM299584v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d5e9257-1041-4a67-8b71-5a914dcb0831/dqc_reference/reference_markers.fasta -out GCF_002995845.1_ASM299584v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:09,020] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:09,025] [INFO] Selected 19 target genomes.
[2024-01-24 12:44:09,026] [INFO] Target genome list was writen to GCF_002995845.1_ASM299584v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:09,138] [INFO] Task started: fastANI
[2024-01-24 12:44:09,139] [INFO] Running command: fastANI --query /var/lib/cwl/stge08b88bf-9c26-4ba6-b2c3-099862332544/GCF_002995845.1_ASM299584v1_genomic.fna.gz --refList GCF_002995845.1_ASM299584v1_genomic.fna/target_genomes.txt --output GCF_002995845.1_ASM299584v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:44:21,613] [INFO] Task succeeded: fastANI
[2024-01-24 12:44:21,614] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5d5e9257-1041-4a67-8b71-5a914dcb0831/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:44:21,614] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5d5e9257-1041-4a67-8b71-5a914dcb0831/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:44:21,630] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:44:21,630] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:44:21,630] [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 luticellarii	strain=DSM 29923	GCA_002995845.1	1691940	1691940	type	True	100.0	1156	1165	95	conclusive
Clostridium kluyveri	strain=NBRC 12016	GCA_000010265.1	1534	1534	type	True	79.0849	336	1165	95	below_threshold
Clostridium kluyveri	strain=DSM 555	GCA_000016505.1	1534	1534	type	True	79.0466	338	1165	95	below_threshold
Clostridium autoethanogenum	strain=DSM 10061	GCA_000484505.2	84023	84023	suspected-type	True	78.6007	332	1165	95	below_threshold
Clostridium autoethanogenum	strain=JA1-1	GCA_002189005.1	84023	84023	suspected-type	True	78.5761	334	1165	95	below_threshold
Clostridium ljungdahlii	strain=DSM 13528	GCA_000143685.1	1538	1538	suspected-type	True	78.533	348	1165	95	below_threshold
Clostridium autoethanogenum	strain=DSM 10061	GCA_000427255.1	84023	84023	suspected-type	True	78.5039	333	1165	95	below_threshold
Clostridium scatologenes	strain=ATCC 25775	GCA_000968375.1	1548	1548	type	True	77.3001	181	1165	95	below_threshold
Clostridium carboxidivorans	strain=P7	GCA_001038625.1	217159	217159	type	True	77.2876	188	1165	95	below_threshold
Clostridium algifaecis	strain=DSM 28783	GCA_017874415.1	1472040	1472040	type	True	77.2617	206	1165	95	below_threshold
Clostridium liquoris	strain=DSM 100320	GCA_002995785.1	1289519	1289519	type	True	77.1296	78	1165	95	below_threshold
Clostridium thailandense	strain=PL3	GCA_019207025.1	2794346	2794346	type	True	76.8562	152	1165	95	below_threshold
Clostridium pasteurianum	strain=DSM 525	GCA_000807255.1	1501	1501	type	True	76.664	113	1165	95	below_threshold
Clostridium sporogenes	strain=DSM 795	GCA_001020205.1	1509	1509	type	True	76.0439	98	1165	95	below_threshold
Clostridium sporogenes	strain=NCIMB 10696	GCA_000973705.1	1509	1509	type	True	76.0126	94	1165	95	below_threshold
Clostridium sporogenes	strain=NCTC13020	GCA_900461305.1	1509	1509	type	True	75.9638	97	1165	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:44:21,632] [INFO] DFAST Taxonomy check result was written to GCF_002995845.1_ASM299584v1_genomic.fna/tc_result.tsv
[2024-01-24 12:44:21,633] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:44:21,633] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:44:21,633] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5d5e9257-1041-4a67-8b71-5a914dcb0831/dqc_reference/checkm_data
[2024-01-24 12:44:21,634] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:44:21,678] [INFO] Task started: CheckM
[2024-01-24 12:44:21,678] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002995845.1_ASM299584v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002995845.1_ASM299584v1_genomic.fna/checkm_input GCF_002995845.1_ASM299584v1_genomic.fna/checkm_result
[2024-01-24 12:44:49,337] [INFO] Task succeeded: CheckM
[2024-01-24 12:44:49,339] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:44:49,360] [INFO] ===== Completeness check finished =====
[2024-01-24 12:44:49,360] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:44:49,361] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002995845.1_ASM299584v1_genomic.fna/markers.fasta)
[2024-01-24 12:44:49,361] [INFO] Task started: Blastn
[2024-01-24 12:44:49,362] [INFO] Running command: blastn -query GCF_002995845.1_ASM299584v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d5e9257-1041-4a67-8b71-5a914dcb0831/dqc_reference/reference_markers_gtdb.fasta -out GCF_002995845.1_ASM299584v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:50,223] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:50,226] [INFO] Selected 12 target genomes.
[2024-01-24 12:44:50,226] [INFO] Target genome list was writen to GCF_002995845.1_ASM299584v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:44:50,281] [INFO] Task started: fastANI
[2024-01-24 12:44:50,282] [INFO] Running command: fastANI --query /var/lib/cwl/stge08b88bf-9c26-4ba6-b2c3-099862332544/GCF_002995845.1_ASM299584v1_genomic.fna.gz --refList GCF_002995845.1_ASM299584v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002995845.1_ASM299584v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:44:59,222] [INFO] Task succeeded: fastANI
[2024-01-24 12:44:59,233] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:44:59,234] [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_002995845.1	s__Clostridium_B luticellarii	100.0	1156	1165	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
GCA_902809985.1	s__Clostridium_B sp902809985	84.085	804	1165	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	-
GCA_903789665.1	s__Clostridium_B sp003497125	80.629	601	1165	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_B	95.0	99.52	99.48	0.90	0.85	3	-
GCF_000016505.1	s__Clostridium_B kluyveri	79.0734	336	1165	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_001675165.1	s__Clostridium_B ragsdalei	78.601	340	1165	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_004006395.2	s__Clostridium_B sp004006395	78.5768	357	1165	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	78.5114	351	1165	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_001636845.1	s__Clostridium_B ljungdahlii_A	78.4629	345	1165	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_000968375.1	s__Clostridium_AM scatologenes	77.2921	180	1165	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	-
GCF_017874415.1	s__Clostridium_B algifaecis	77.2879	204	1165	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_002995785.1	s__Clostridium_AO liquoris	77.16	77	1165	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AO	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019207025.1	s__Clostridium_AM sp019207025	76.8562	152	1165	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AM	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:44:59,235] [INFO] GTDB search result was written to GCF_002995845.1_ASM299584v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:44:59,236] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:44:59,239] [INFO] DFAST_QC result json was written to GCF_002995845.1_ASM299584v1_genomic.fna/dqc_result.json
[2024-01-24 12:44:59,240] [INFO] DFAST_QC completed!
[2024-01-24 12:44:59,240] [INFO] Total running time: 0h1m5s