[2024-01-24 14:53:49,635] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:53:49,638] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:53:49,638] [INFO] DQC Reference Directory: /var/lib/cwl/stgb463c18c-6226-4198-be0d-d184eb07df6f/dqc_reference
[2024-01-24 14:53:50,925] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:53:50,926] [INFO] Task started: Prodigal
[2024-01-24 14:53:50,926] [INFO] Running command: gunzip -c /var/lib/cwl/stgd707f91f-4e9d-432d-99cf-4f90c8ecac05/GCF_005405305.1_ASM540530v1_genomic.fna.gz | prodigal -d GCF_005405305.1_ASM540530v1_genomic.fna/cds.fna -a GCF_005405305.1_ASM540530v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:53:56,032] [INFO] Task succeeded: Prodigal
[2024-01-24 14:53:56,033] [INFO] Task started: HMMsearch
[2024-01-24 14:53:56,033] [INFO] Running command: hmmsearch --tblout GCF_005405305.1_ASM540530v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb463c18c-6226-4198-be0d-d184eb07df6f/dqc_reference/reference_markers.hmm GCF_005405305.1_ASM540530v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:53:56,271] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:53:56,273] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd707f91f-4e9d-432d-99cf-4f90c8ecac05/GCF_005405305.1_ASM540530v1_genomic.fna.gz]
[2024-01-24 14:53:56,299] [INFO] Query marker FASTA was written to GCF_005405305.1_ASM540530v1_genomic.fna/markers.fasta
[2024-01-24 14:53:56,300] [INFO] Task started: Blastn
[2024-01-24 14:53:56,300] [INFO] Running command: blastn -query GCF_005405305.1_ASM540530v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb463c18c-6226-4198-be0d-d184eb07df6f/dqc_reference/reference_markers.fasta -out GCF_005405305.1_ASM540530v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:53:56,898] [INFO] Task succeeded: Blastn
[2024-01-24 14:53:56,901] [INFO] Selected 11 target genomes.
[2024-01-24 14:53:56,901] [INFO] Target genome list was writen to GCF_005405305.1_ASM540530v1_genomic.fna/target_genomes.txt
[2024-01-24 14:53:56,922] [INFO] Task started: fastANI
[2024-01-24 14:53:56,922] [INFO] Running command: fastANI --query /var/lib/cwl/stgd707f91f-4e9d-432d-99cf-4f90c8ecac05/GCF_005405305.1_ASM540530v1_genomic.fna.gz --refList GCF_005405305.1_ASM540530v1_genomic.fna/target_genomes.txt --output GCF_005405305.1_ASM540530v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:54:03,333] [INFO] Task succeeded: fastANI
[2024-01-24 14:54:03,333] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb463c18c-6226-4198-be0d-d184eb07df6f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:54:03,334] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb463c18c-6226-4198-be0d-d184eb07df6f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:54:03,348] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:54:03,348] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:54:03,348] [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
Companilactobacillus formosensis	strain=NBRC 109509	GCA_005405305.1	1617889	1617889	type	True	100.0	811	812	95	conclusive
Companilactobacillus formosensis	strain=S215	GCA_003573535.1	1617889	1617889	type	True	99.9933	806	812	95	conclusive
Companilactobacillus pabuli	strain=NFFJ11	GCA_014058425.1	2714036	2714036	type	True	92.703	715	812	95	below_threshold
Companilactobacillus farciminis	strain=DSM 20184	GCA_001434775.1	1612	1612	suspected-type	True	91.1849	683	812	95	below_threshold
Companilactobacillus farciminis	strain=DSM 20184	GCA_002706745.1	1612	1612	suspected-type	True	91.1674	702	812	95	below_threshold
Companilactobacillus farciminis	strain=ATCC 29644	GCA_004354695.1	1612	1612	suspected-type	True	91.1503	690	812	95	below_threshold
Companilactobacillus kimchii	strain=DSM 13961	GCA_009764365.1	2801452	2801452	type	True	81.6971	434	812	95	below_threshold
Companilactobacillus paralimentarius	strain=DSM 13238	GCA_009764345.1	83526	83526	type	True	81.6649	410	812	95	below_threshold
Companilactobacillus mishanensis	strain=256-3	GCA_003946505.1	2486008	2486008	type	True	78.8663	198	812	95	below_threshold
Companilactobacillus allii	strain=WiKim39	GCA_023923085.1	1847728	1847728	type	True	78.7807	268	812	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:54:03,349] [INFO] DFAST Taxonomy check result was written to GCF_005405305.1_ASM540530v1_genomic.fna/tc_result.tsv
[2024-01-24 14:54:03,350] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:54:03,350] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:54:03,350] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb463c18c-6226-4198-be0d-d184eb07df6f/dqc_reference/checkm_data
[2024-01-24 14:54:03,352] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:54:03,378] [INFO] Task started: CheckM
[2024-01-24 14:54:03,378] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005405305.1_ASM540530v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005405305.1_ASM540530v1_genomic.fna/checkm_input GCF_005405305.1_ASM540530v1_genomic.fna/checkm_result
[2024-01-24 14:54:26,262] [INFO] Task succeeded: CheckM
[2024-01-24 14:54:26,264] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:54:26,286] [INFO] ===== Completeness check finished =====
[2024-01-24 14:54:26,286] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:54:26,287] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005405305.1_ASM540530v1_genomic.fna/markers.fasta)
[2024-01-24 14:54:26,287] [INFO] Task started: Blastn
[2024-01-24 14:54:26,287] [INFO] Running command: blastn -query GCF_005405305.1_ASM540530v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb463c18c-6226-4198-be0d-d184eb07df6f/dqc_reference/reference_markers_gtdb.fasta -out GCF_005405305.1_ASM540530v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:54:27,020] [INFO] Task succeeded: Blastn
[2024-01-24 14:54:27,027] [INFO] Selected 8 target genomes.
[2024-01-24 14:54:27,027] [INFO] Target genome list was writen to GCF_005405305.1_ASM540530v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:54:27,035] [INFO] Task started: fastANI
[2024-01-24 14:54:27,036] [INFO] Running command: fastANI --query /var/lib/cwl/stgd707f91f-4e9d-432d-99cf-4f90c8ecac05/GCF_005405305.1_ASM540530v1_genomic.fna.gz --refList GCF_005405305.1_ASM540530v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005405305.1_ASM540530v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:54:32,409] [INFO] Task succeeded: fastANI
[2024-01-24 14:54:32,417] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:54:32,417] [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_005405305.1	s__Companilactobacillus formosensis	100.0	811	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_014058425.1	s__Companilactobacillus pabuli	92.7285	714	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	99.23	98.09	0.94	0.87	5	-
GCF_002706745.1	s__Companilactobacillus farciminis	91.1596	703	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	98.95	96.63	0.97	0.92	6	-
GCF_001435505.1	s__Companilactobacillus futsaii	90.4313	653	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	99.20	98.55	0.91	0.87	7	-
GCF_003967595.1	s__Companilactobacillus musae	83.024	479	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001435815.1	s__Companilactobacillus nantensis	82.4005	474	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000831645.3	s__Companilactobacillus heilongjiangensis	82.229	485	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009600985.1	s__Companilactobacillus halodurans	81.8972	466	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	99.75	99.75	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:54:32,419] [INFO] GTDB search result was written to GCF_005405305.1_ASM540530v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:54:32,419] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:54:32,422] [INFO] DFAST_QC result json was written to GCF_005405305.1_ASM540530v1_genomic.fna/dqc_result.json
[2024-01-24 14:54:32,422] [INFO] DFAST_QC completed!
[2024-01-24 14:54:32,423] [INFO] Total running time: 0h0m43s