[2024-01-24 14:13:15,645] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:13:15,647] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:13:15,647] [INFO] DQC Reference Directory: /var/lib/cwl/stgda07195e-b017-4f30-81b1-e2343d524ee5/dqc_reference
[2024-01-24 14:13:16,914] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:13:16,915] [INFO] Task started: Prodigal
[2024-01-24 14:13:16,916] [INFO] Running command: gunzip -c /var/lib/cwl/stg4414ccc1-1055-42e2-baac-72b311ca2de8/GCF_001484725.1_ASM148472v1_genomic.fna.gz | prodigal -d GCF_001484725.1_ASM148472v1_genomic.fna/cds.fna -a GCF_001484725.1_ASM148472v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:13:24,576] [INFO] Task succeeded: Prodigal
[2024-01-24 14:13:24,576] [INFO] Task started: HMMsearch
[2024-01-24 14:13:24,576] [INFO] Running command: hmmsearch --tblout GCF_001484725.1_ASM148472v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgda07195e-b017-4f30-81b1-e2343d524ee5/dqc_reference/reference_markers.hmm GCF_001484725.1_ASM148472v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:13:24,903] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:13:24,905] [INFO] Found 6/6 markers.
[2024-01-24 14:13:24,944] [INFO] Query marker FASTA was written to GCF_001484725.1_ASM148472v1_genomic.fna/markers.fasta
[2024-01-24 14:13:24,944] [INFO] Task started: Blastn
[2024-01-24 14:13:24,945] [INFO] Running command: blastn -query GCF_001484725.1_ASM148472v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgda07195e-b017-4f30-81b1-e2343d524ee5/dqc_reference/reference_markers.fasta -out GCF_001484725.1_ASM148472v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:25,528] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:25,532] [INFO] Selected 11 target genomes.
[2024-01-24 14:13:25,533] [INFO] Target genome list was writen to GCF_001484725.1_ASM148472v1_genomic.fna/target_genomes.txt
[2024-01-24 14:13:25,547] [INFO] Task started: fastANI
[2024-01-24 14:13:25,547] [INFO] Running command: fastANI --query /var/lib/cwl/stg4414ccc1-1055-42e2-baac-72b311ca2de8/GCF_001484725.1_ASM148472v1_genomic.fna.gz --refList GCF_001484725.1_ASM148472v1_genomic.fna/target_genomes.txt --output GCF_001484725.1_ASM148472v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:39,749] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:39,750] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgda07195e-b017-4f30-81b1-e2343d524ee5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:39,750] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgda07195e-b017-4f30-81b1-e2343d524ee5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:39,760] [INFO] Found 10 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 14:13:39,761] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:13:39,761] [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 autoethanogenum	strain=DSM 10061	GCA_001484725.1	84023	84023	suspected-type	True	100.0	1449	1450	95	inconclusive
Clostridium autoethanogenum	strain=DSM 10061	GCA_000484505.2	84023	84023	suspected-type	True	99.9952	1450	1450	95	inconclusive
Clostridium autoethanogenum	strain=JA1-1	GCA_002189005.1	84023	84023	suspected-type	True	99.9792	1426	1450	95	inconclusive
Clostridium autoethanogenum	strain=DSM 10061	GCA_000427255.1	84023	84023	suspected-type	True	99.9573	1383	1450	95	inconclusive
Clostridium ljungdahlii	strain=DSM 13528	GCA_000143685.1	1538	1538	suspected-type	True	99.0044	1356	1450	95	inconclusive
Clostridium muellerianum	strain=P21	GCA_012926525.1	2716538	2716538	type	True	79.3631	442	1450	95	below_threshold
Clostridium kluyveri	strain=DSM 555	GCA_000016505.1	1534	1534	type	True	78.994	418	1450	95	below_threshold
Clostridium kluyveri	strain=NBRC 12016	GCA_000010265.1	1534	1534	type	True	78.9286	418	1450	95	below_threshold
Clostridium thailandense	strain=PL3	GCA_019207025.1	2794346	2794346	type	True	78.0052	353	1450	95	below_threshold
Crassaminicella profunda	strain=Ra1766H	GCA_019884785.1	1286698	1286698	type	True	77.1289	75	1450	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:39,762] [INFO] DFAST Taxonomy check result was written to GCF_001484725.1_ASM148472v1_genomic.fna/tc_result.tsv
[2024-01-24 14:13:39,763] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:39,763] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:39,763] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgda07195e-b017-4f30-81b1-e2343d524ee5/dqc_reference/checkm_data
[2024-01-24 14:13:39,765] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:39,813] [INFO] Task started: CheckM
[2024-01-24 14:13:39,813] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001484725.1_ASM148472v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001484725.1_ASM148472v1_genomic.fna/checkm_input GCF_001484725.1_ASM148472v1_genomic.fna/checkm_result
[2024-01-24 14:14:08,568] [INFO] Task succeeded: CheckM
[2024-01-24 14:14:08,570] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:14:08,607] [INFO] ===== Completeness check finished =====
[2024-01-24 14:14:08,608] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:14:08,608] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001484725.1_ASM148472v1_genomic.fna/markers.fasta)
[2024-01-24 14:14:08,609] [INFO] Task started: Blastn
[2024-01-24 14:14:08,609] [INFO] Running command: blastn -query GCF_001484725.1_ASM148472v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgda07195e-b017-4f30-81b1-e2343d524ee5/dqc_reference/reference_markers_gtdb.fasta -out GCF_001484725.1_ASM148472v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:09,341] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:09,345] [INFO] Selected 9 target genomes.
[2024-01-24 14:14:09,346] [INFO] Target genome list was writen to GCF_001484725.1_ASM148472v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:14:09,356] [INFO] Task started: fastANI
[2024-01-24 14:14:09,356] [INFO] Running command: fastANI --query /var/lib/cwl/stg4414ccc1-1055-42e2-baac-72b311ca2de8/GCF_001484725.1_ASM148472v1_genomic.fna.gz --refList GCF_001484725.1_ASM148472v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001484725.1_ASM148472v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:14:20,472] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:20,486] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:14:20,486] [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	98.9899	1358	1450	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	94.831	1168	1450	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	94.3406	1114	1450	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	94.0105	1184	1450	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	79.3228	499	1450	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	78.9776	419	1450	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	78.7296	343	1450	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	78.3765	368	1450	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 14:14:20,488] [INFO] GTDB search result was written to GCF_001484725.1_ASM148472v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:14:20,489] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:14:20,492] [INFO] DFAST_QC result json was written to GCF_001484725.1_ASM148472v1_genomic.fna/dqc_result.json
[2024-01-24 14:14:20,492] [INFO] DFAST_QC completed!
[2024-01-24 14:14:20,493] [INFO] Total running time: 0h1m5s