[2024-01-24 13:31:44,154] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:44,157] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:44,157] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe57a57e-0dc0-4211-a912-a49908ad6a31/dqc_reference
[2024-01-24 13:31:45,423] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:45,424] [INFO] Task started: Prodigal
[2024-01-24 13:31:45,424] [INFO] Running command: gunzip -c /var/lib/cwl/stgb7d9ec6f-b17c-424c-9200-cf3f9f55403a/GCF_009831105.1_ASM983110v1_genomic.fna.gz | prodigal -d GCF_009831105.1_ASM983110v1_genomic.fna/cds.fna -a GCF_009831105.1_ASM983110v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:51,120] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:51,121] [INFO] Task started: HMMsearch
[2024-01-24 13:31:51,121] [INFO] Running command: hmmsearch --tblout GCF_009831105.1_ASM983110v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe57a57e-0dc0-4211-a912-a49908ad6a31/dqc_reference/reference_markers.hmm GCF_009831105.1_ASM983110v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:51,379] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:51,381] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb7d9ec6f-b17c-424c-9200-cf3f9f55403a/GCF_009831105.1_ASM983110v1_genomic.fna.gz]
[2024-01-24 13:31:51,411] [INFO] Query marker FASTA was written to GCF_009831105.1_ASM983110v1_genomic.fna/markers.fasta
[2024-01-24 13:31:51,412] [INFO] Task started: Blastn
[2024-01-24 13:31:51,412] [INFO] Running command: blastn -query GCF_009831105.1_ASM983110v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe57a57e-0dc0-4211-a912-a49908ad6a31/dqc_reference/reference_markers.fasta -out GCF_009831105.1_ASM983110v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:52,041] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:52,046] [INFO] Selected 23 target genomes.
[2024-01-24 13:31:52,047] [INFO] Target genome list was writen to GCF_009831105.1_ASM983110v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:52,069] [INFO] Task started: fastANI
[2024-01-24 13:31:52,070] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7d9ec6f-b17c-424c-9200-cf3f9f55403a/GCF_009831105.1_ASM983110v1_genomic.fna.gz --refList GCF_009831105.1_ASM983110v1_genomic.fna/target_genomes.txt --output GCF_009831105.1_ASM983110v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:04,029] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:04,030] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe57a57e-0dc0-4211-a912-a49908ad6a31/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:04,030] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe57a57e-0dc0-4211-a912-a49908ad6a31/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:04,037] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:04,037] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:04,037] [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
Copranaerobaculum intestinale	strain=DONG20-135	GCA_009831105.1	2692629	2692629	type	True	100.0	759	760	95	conclusive
Amedibacillus dolichus	strain=DSM 3991	GCA_000154285.1	31971	31971	type	True	80.4384	65	760	95	below_threshold
Longicatena caecimuris	strain=DSM 29481	GCA_024622185.1	1796635	1796635	type	True	78.2769	53	760	95	below_threshold
Massilicoli timonensis	strain=Marseille-P3755	GCA_900199515.1	2015901	2015901	type	True	77.3128	83	760	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:04,041] [INFO] DFAST Taxonomy check result was written to GCF_009831105.1_ASM983110v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:04,042] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:04,042] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:04,043] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe57a57e-0dc0-4211-a912-a49908ad6a31/dqc_reference/checkm_data
[2024-01-24 13:32:04,045] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:04,076] [INFO] Task started: CheckM
[2024-01-24 13:32:04,076] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009831105.1_ASM983110v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009831105.1_ASM983110v1_genomic.fna/checkm_input GCF_009831105.1_ASM983110v1_genomic.fna/checkm_result
[2024-01-24 13:32:30,171] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:30,173] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:30,198] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:30,198] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:30,199] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009831105.1_ASM983110v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:30,199] [INFO] Task started: Blastn
[2024-01-24 13:32:30,200] [INFO] Running command: blastn -query GCF_009831105.1_ASM983110v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe57a57e-0dc0-4211-a912-a49908ad6a31/dqc_reference/reference_markers_gtdb.fasta -out GCF_009831105.1_ASM983110v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:31,052] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:31,055] [INFO] Selected 23 target genomes.
[2024-01-24 13:32:31,055] [INFO] Target genome list was writen to GCF_009831105.1_ASM983110v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:31,136] [INFO] Task started: fastANI
[2024-01-24 13:32:31,137] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7d9ec6f-b17c-424c-9200-cf3f9f55403a/GCF_009831105.1_ASM983110v1_genomic.fna.gz --refList GCF_009831105.1_ASM983110v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009831105.1_ASM983110v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:32:41,973] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:41,985] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:32:41,986] [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
GCA_009831105.1	s__DONG20-135 sp009831105	100.0	759	760	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__DONG20-135	95.0	98.89	98.89	0.93	0.93	2	conclusive
GCF_014337235.1	s__NSJ-61 sp003433845	81.952	63	760	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__NSJ-61	95.0	99.54	98.10	0.85	0.77	12	-
GCF_000154285.1	s__Amedibacillus dolichus	80.5924	63	760	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Amedibacillus	95.0	99.06	98.73	0.91	0.85	7	-
GCA_003481775.1	s__Clostridium_AQ sp003481775	80.1895	92	760	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Clostridium_AQ	95.0	99.27	97.98	0.91	0.82	5	-
GCF_004341945.1	s__Longicatena caecimuris	78.3111	52	760	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Longicatena	95.0	98.56	98.14	0.91	0.88	21	-
GCF_900199515.1	s__Massilicoli timonensis	77.287	81	760	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Massilicoli	95.0	98.84	98.66	0.94	0.87	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:32:41,988] [INFO] GTDB search result was written to GCF_009831105.1_ASM983110v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:32:41,988] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:32:41,991] [INFO] DFAST_QC result json was written to GCF_009831105.1_ASM983110v1_genomic.fna/dqc_result.json
[2024-01-24 13:32:41,991] [INFO] DFAST_QC completed!
[2024-01-24 13:32:41,991] [INFO] Total running time: 0h0m58s