[2024-01-25 17:40:20,505] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:40:20,506] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:40:20,507] [INFO] DQC Reference Directory: /var/lib/cwl/stgd16d3ea6-46b4-4fd4-be0f-c35c6659bf9c/dqc_reference
[2024-01-25 17:40:21,676] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:40:21,677] [INFO] Task started: Prodigal
[2024-01-25 17:40:21,677] [INFO] Running command: gunzip -c /var/lib/cwl/stg964609a6-6904-473e-b208-920aa2c11270/GCF_014641195.1_ASM1464119v1_genomic.fna.gz | prodigal -d GCF_014641195.1_ASM1464119v1_genomic.fna/cds.fna -a GCF_014641195.1_ASM1464119v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:40:31,008] [INFO] Task succeeded: Prodigal
[2024-01-25 17:40:31,009] [INFO] Task started: HMMsearch
[2024-01-25 17:40:31,009] [INFO] Running command: hmmsearch --tblout GCF_014641195.1_ASM1464119v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd16d3ea6-46b4-4fd4-be0f-c35c6659bf9c/dqc_reference/reference_markers.hmm GCF_014641195.1_ASM1464119v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:40:31,211] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:40:31,213] [INFO] Found 6/6 markers.
[2024-01-25 17:40:31,244] [INFO] Query marker FASTA was written to GCF_014641195.1_ASM1464119v1_genomic.fna/markers.fasta
[2024-01-25 17:40:31,244] [INFO] Task started: Blastn
[2024-01-25 17:40:31,244] [INFO] Running command: blastn -query GCF_014641195.1_ASM1464119v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd16d3ea6-46b4-4fd4-be0f-c35c6659bf9c/dqc_reference/reference_markers.fasta -out GCF_014641195.1_ASM1464119v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:40:31,824] [INFO] Task succeeded: Blastn
[2024-01-25 17:40:31,827] [INFO] Selected 18 target genomes.
[2024-01-25 17:40:31,828] [INFO] Target genome list was writen to GCF_014641195.1_ASM1464119v1_genomic.fna/target_genomes.txt
[2024-01-25 17:40:31,857] [INFO] Task started: fastANI
[2024-01-25 17:40:31,858] [INFO] Running command: fastANI --query /var/lib/cwl/stg964609a6-6904-473e-b208-920aa2c11270/GCF_014641195.1_ASM1464119v1_genomic.fna.gz --refList GCF_014641195.1_ASM1464119v1_genomic.fna/target_genomes.txt --output GCF_014641195.1_ASM1464119v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:40:46,002] [INFO] Task succeeded: fastANI
[2024-01-25 17:40:46,002] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd16d3ea6-46b4-4fd4-be0f-c35c6659bf9c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:40:46,003] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd16d3ea6-46b4-4fd4-be0f-c35c6659bf9c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:40:46,010] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:40:46,011] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:40:46,011] [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
Marinithermofilum abyssi	strain=CGMCC 1.15179	GCA_014641195.1	1571185	1571185	type	True	100.0	1150	1153	95	conclusive
Polycladomyces abyssicola	strain=JIR-001	GCA_018326425.1	1125966	1125966	type	True	78.9414	148	1153	95	below_threshold
Planifilum fulgidum	strain=DSM 44945	GCA_900113175.1	201973	201973	type	True	77.1388	73	1153	95	below_threshold
Kroppenstedtia pulmonis	strain=W9323	GCA_013265585.1	1380685	1380685	type	True	77.1313	84	1153	95	below_threshold
Kroppenstedtia eburnea	strain=DSM 45196	GCA_900156615.1	714067	714067	type	True	76.9032	145	1153	95	below_threshold
Kroppenstedtia eburnea	strain=DSM 45196	GCA_013282215.1	714067	714067	type	True	76.8737	147	1153	95	below_threshold
Lihuaxuella thermophila	strain=DSM 46701	GCA_900110165.1	1173111	1173111	type	True	76.8734	74	1153	95	below_threshold
Desmospora activa	strain=DSM 45169	GCA_003046315.1	500615	500615	type	True	76.5688	116	1153	95	below_threshold
Melghirimyces algeriensis	strain=DSM 45474	GCA_900182565.1	910412	910412	type	True	76.4941	93	1153	95	below_threshold
Staphylospora marina	strain=SCSIO 07575	GCA_003856495.1	2490858	2490858	type	True	76.2427	69	1153	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:40:46,015] [INFO] DFAST Taxonomy check result was written to GCF_014641195.1_ASM1464119v1_genomic.fna/tc_result.tsv
[2024-01-25 17:40:46,015] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:40:46,016] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:40:46,016] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd16d3ea6-46b4-4fd4-be0f-c35c6659bf9c/dqc_reference/checkm_data
[2024-01-25 17:40:46,017] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:40:46,053] [INFO] Task started: CheckM
[2024-01-25 17:40:46,053] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014641195.1_ASM1464119v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014641195.1_ASM1464119v1_genomic.fna/checkm_input GCF_014641195.1_ASM1464119v1_genomic.fna/checkm_result
[2024-01-25 17:41:15,924] [INFO] Task succeeded: CheckM
[2024-01-25 17:41:15,926] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:41:15,946] [INFO] ===== Completeness check finished =====
[2024-01-25 17:41:15,946] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:41:15,947] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014641195.1_ASM1464119v1_genomic.fna/markers.fasta)
[2024-01-25 17:41:15,947] [INFO] Task started: Blastn
[2024-01-25 17:41:15,947] [INFO] Running command: blastn -query GCF_014641195.1_ASM1464119v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd16d3ea6-46b4-4fd4-be0f-c35c6659bf9c/dqc_reference/reference_markers_gtdb.fasta -out GCF_014641195.1_ASM1464119v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:41:16,883] [INFO] Task succeeded: Blastn
[2024-01-25 17:41:16,886] [INFO] Selected 19 target genomes.
[2024-01-25 17:41:16,886] [INFO] Target genome list was writen to GCF_014641195.1_ASM1464119v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:41:16,900] [INFO] Task started: fastANI
[2024-01-25 17:41:16,901] [INFO] Running command: fastANI --query /var/lib/cwl/stg964609a6-6904-473e-b208-920aa2c11270/GCF_014641195.1_ASM1464119v1_genomic.fna.gz --refList GCF_014641195.1_ASM1464119v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014641195.1_ASM1464119v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:41:31,927] [INFO] Task succeeded: fastANI
[2024-01-25 17:41:31,935] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:41:31,935] [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_014641195.1	s__Marinithermofilum abyssi	100.0	1150	1153	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__DSM-45169;g__Marinithermofilum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018326425.1	s__Polycladomyces abyssicola	78.9095	150	1153	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__JIR-001;g__Polycladomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016055185.1	s__Paenactinomyces guangxiensis	77.4957	52	1153	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__Thermoactinomycetaceae;g__Paenactinomyces	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900113175.1	s__Planifilum fulgidum	77.1388	73	1153	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__DSM-44946;g__Planifilum	95.0	99.34	99.26	0.97	0.97	3	-
GCF_013265585.1	s__Kroppenstedtia_A pulmonis	77.1119	83	1153	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__DSM-45169;g__Kroppenstedtia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110165.1	s__Lihuaxuella thermophila	76.8734	74	1153	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__Thermoactinomycetaceae;g__Lihuaxuella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013282215.1	s__Kroppenstedtia eburnea	76.8396	148	1153	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__DSM-45169;g__Kroppenstedtia	95.0	99.43	98.85	0.98	0.95	3	-
GCF_003046315.1	s__Desmospora activa	76.5688	116	1153	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__DSM-45169;g__Desmospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900182565.1	s__Melghirimyces algeriensis	76.4734	94	1153	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__DSM-45169;g__Melghirimyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003856495.1	s__Staphylospora marina	76.2427	69	1153	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__Thermoactinomycetaceae;g__Staphylospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:41:31,937] [INFO] GTDB search result was written to GCF_014641195.1_ASM1464119v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:41:31,937] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:41:31,940] [INFO] DFAST_QC result json was written to GCF_014641195.1_ASM1464119v1_genomic.fna/dqc_result.json
[2024-01-25 17:41:31,940] [INFO] DFAST_QC completed!
[2024-01-25 17:41:31,940] [INFO] Total running time: 0h1m11s