[2024-01-24 13:55:18,457] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:18,460] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:18,460] [INFO] DQC Reference Directory: /var/lib/cwl/stgc7a83ba1-1b31-48d2-8f60-c41599351fdc/dqc_reference
[2024-01-24 13:55:19,831] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:19,832] [INFO] Task started: Prodigal
[2024-01-24 13:55:19,832] [INFO] Running command: gunzip -c /var/lib/cwl/stgf4705f6b-e299-4fdd-aeb6-a35f365aa455/GCF_000143685.1_ASM14368v1_genomic.fna.gz | prodigal -d GCF_000143685.1_ASM14368v1_genomic.fna/cds.fna -a GCF_000143685.1_ASM14368v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:28,403] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:28,403] [INFO] Task started: HMMsearch
[2024-01-24 13:55:28,404] [INFO] Running command: hmmsearch --tblout GCF_000143685.1_ASM14368v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc7a83ba1-1b31-48d2-8f60-c41599351fdc/dqc_reference/reference_markers.hmm GCF_000143685.1_ASM14368v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:28,825] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:28,826] [INFO] Found 6/6 markers.
[2024-01-24 13:55:28,867] [INFO] Query marker FASTA was written to GCF_000143685.1_ASM14368v1_genomic.fna/markers.fasta
[2024-01-24 13:55:28,867] [INFO] Task started: Blastn
[2024-01-24 13:55:28,867] [INFO] Running command: blastn -query GCF_000143685.1_ASM14368v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7a83ba1-1b31-48d2-8f60-c41599351fdc/dqc_reference/reference_markers.fasta -out GCF_000143685.1_ASM14368v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:29,548] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:29,551] [INFO] Selected 12 target genomes.
[2024-01-24 13:55:29,552] [INFO] Target genome list was writen to GCF_000143685.1_ASM14368v1_genomic.fna/target_genomes.txt
[2024-01-24 13:55:29,562] [INFO] Task started: fastANI
[2024-01-24 13:55:29,562] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4705f6b-e299-4fdd-aeb6-a35f365aa455/GCF_000143685.1_ASM14368v1_genomic.fna.gz --refList GCF_000143685.1_ASM14368v1_genomic.fna/target_genomes.txt --output GCF_000143685.1_ASM14368v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:55:45,664] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:45,665] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc7a83ba1-1b31-48d2-8f60-c41599351fdc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:55:45,665] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc7a83ba1-1b31-48d2-8f60-c41599351fdc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:55:45,675] [INFO] Found 11 fastANI hits (6 hits with ANI > threshold)
[2024-01-24 13:55:45,676] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:55:45,676] [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 ljungdahlii	strain=DSM 13528	GCA_000143685.1	1538	1538	suspected-type	True	100.0	1540	1543	95	inconclusive
Clostridium ljungdahlii	strain=PETC	GCA_001636855.1	1538	1538	suspected-type	True	99.9531	1504	1543	95	inconclusive
Clostridium autoethanogenum	strain=DSM 10061	GCA_000484505.2	84023	84023	suspected-type	True	98.9529	1354	1543	95	inconclusive
Clostridium autoethanogenum	strain=JA1-1	GCA_002189005.1	84023	84023	suspected-type	True	98.9488	1334	1543	95	inconclusive
Clostridium autoethanogenum	strain=DSM 10061	GCA_000427255.1	84023	84023	suspected-type	True	98.9387	1293	1543	95	inconclusive
Clostridium autoethanogenum	strain=DSM 10061	GCA_001484725.1	84023	84023	suspected-type	True	98.9278	1358	1543	95	inconclusive
Clostridium muellerianum	strain=P21	GCA_012926525.1	2716538	2716538	type	True	79.6662	463	1543	95	below_threshold
Clostridium kluyveri	strain=DSM 555	GCA_000016505.1	1534	1534	type	True	79.0989	426	1543	95	below_threshold
Clostridium kluyveri	strain=NBRC 12016	GCA_000010265.1	1534	1534	type	True	79.0579	421	1543	95	below_threshold
Clostridium thailandense	strain=PL3	GCA_019207025.1	2794346	2794346	type	True	77.9408	375	1543	95	below_threshold
Crassaminicella profunda	strain=Ra1766H	GCA_019884785.1	1286698	1286698	type	True	76.7206	85	1543	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:55:45,678] [INFO] DFAST Taxonomy check result was written to GCF_000143685.1_ASM14368v1_genomic.fna/tc_result.tsv
[2024-01-24 13:55:45,678] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:55:45,678] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:55:45,679] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc7a83ba1-1b31-48d2-8f60-c41599351fdc/dqc_reference/checkm_data
[2024-01-24 13:55:45,680] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:55:45,727] [INFO] Task started: CheckM
[2024-01-24 13:55:45,727] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000143685.1_ASM14368v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000143685.1_ASM14368v1_genomic.fna/checkm_input GCF_000143685.1_ASM14368v1_genomic.fna/checkm_result
[2024-01-24 13:56:15,595] [INFO] Task succeeded: CheckM
[2024-01-24 13:56:15,596] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:56:15,618] [INFO] ===== Completeness check finished =====
[2024-01-24 13:56:15,619] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:56:15,619] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000143685.1_ASM14368v1_genomic.fna/markers.fasta)
[2024-01-24 13:56:15,619] [INFO] Task started: Blastn
[2024-01-24 13:56:15,620] [INFO] Running command: blastn -query GCF_000143685.1_ASM14368v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7a83ba1-1b31-48d2-8f60-c41599351fdc/dqc_reference/reference_markers_gtdb.fasta -out GCF_000143685.1_ASM14368v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:16,392] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:16,395] [INFO] Selected 9 target genomes.
[2024-01-24 13:56:16,395] [INFO] Target genome list was writen to GCF_000143685.1_ASM14368v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:56:16,405] [INFO] Task started: fastANI
[2024-01-24 13:56:16,405] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4705f6b-e299-4fdd-aeb6-a35f365aa455/GCF_000143685.1_ASM14368v1_genomic.fna.gz --refList GCF_000143685.1_ASM14368v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000143685.1_ASM14368v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:56:27,700] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:27,708] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:56:27,708] [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_000143685.1	s__Clostridium_B ljungdahlii	100.0	1539	1543	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	conclusive
GCF_001675165.1	s__Clostridium_B ragsdalei	94.7037	1186	1543	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	94.2094	1150	1543	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_004006395.2	s__Clostridium_B sp004006395	93.9841	1226	1543	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_000633595.2	s__Clostridium_AM drakei	79.5762	492	1543	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AM	96.092	100.00	100.00	1.00	1.00	2	-
GCF_000016505.1	s__Clostridium_B kluyveri	79.1567	423	1543	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_017874415.1	s__Clostridium_B algifaecis	78.981	360	1543	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_002995845.1	s__Clostridium_B luticellarii	78.4016	386	1543	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	-
--------------------------------------------------------------------------------
[2024-01-24 13:56:27,709] [INFO] GTDB search result was written to GCF_000143685.1_ASM14368v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:56:27,710] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:56:27,712] [INFO] DFAST_QC result json was written to GCF_000143685.1_ASM14368v1_genomic.fna/dqc_result.json
[2024-01-24 13:56:27,713] [INFO] DFAST_QC completed!
[2024-01-24 13:56:27,713] [INFO] Total running time: 0h1m9s