[2024-01-24 14:37:47,809] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:37:47,811] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:37:47,811] [INFO] DQC Reference Directory: /var/lib/cwl/stg5d0f3057-3361-4aa7-abc3-18660b2b433c/dqc_reference
[2024-01-24 14:37:50,274] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:37:50,276] [INFO] Task started: Prodigal
[2024-01-24 14:37:50,276] [INFO] Running command: gunzip -c /var/lib/cwl/stgcfa42dd4-1f56-481e-8804-06e1bdc919ab/GCF_003856495.1_ASM385649v1_genomic.fna.gz | prodigal -d GCF_003856495.1_ASM385649v1_genomic.fna/cds.fna -a GCF_003856495.1_ASM385649v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:38:00,228] [INFO] Task succeeded: Prodigal
[2024-01-24 14:38:00,228] [INFO] Task started: HMMsearch
[2024-01-24 14:38:00,228] [INFO] Running command: hmmsearch --tblout GCF_003856495.1_ASM385649v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5d0f3057-3361-4aa7-abc3-18660b2b433c/dqc_reference/reference_markers.hmm GCF_003856495.1_ASM385649v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:38:00,484] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:38:00,486] [INFO] Found 6/6 markers.
[2024-01-24 14:38:00,515] [INFO] Query marker FASTA was written to GCF_003856495.1_ASM385649v1_genomic.fna/markers.fasta
[2024-01-24 14:38:00,516] [INFO] Task started: Blastn
[2024-01-24 14:38:00,516] [INFO] Running command: blastn -query GCF_003856495.1_ASM385649v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d0f3057-3361-4aa7-abc3-18660b2b433c/dqc_reference/reference_markers.fasta -out GCF_003856495.1_ASM385649v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:38:01,186] [INFO] Task succeeded: Blastn
[2024-01-24 14:38:01,191] [INFO] Selected 20 target genomes.
[2024-01-24 14:38:01,191] [INFO] Target genome list was writen to GCF_003856495.1_ASM385649v1_genomic.fna/target_genomes.txt
[2024-01-24 14:38:01,211] [INFO] Task started: fastANI
[2024-01-24 14:38:01,211] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfa42dd4-1f56-481e-8804-06e1bdc919ab/GCF_003856495.1_ASM385649v1_genomic.fna.gz --refList GCF_003856495.1_ASM385649v1_genomic.fna/target_genomes.txt --output GCF_003856495.1_ASM385649v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:38:15,639] [INFO] Task succeeded: fastANI
[2024-01-24 14:38:15,639] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5d0f3057-3361-4aa7-abc3-18660b2b433c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:38:15,639] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5d0f3057-3361-4aa7-abc3-18660b2b433c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:38:15,648] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:38:15,649] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:38:15,649] [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
Staphylospora marina	strain=SCSIO 07575	GCA_003856495.1	2490858	2490858	type	True	100.0	916	916	95	conclusive
Polycladomyces abyssicola	strain=JIR-001	GCA_018326425.1	1125966	1125966	type	True	78.1208	82	916	95	below_threshold
Thermoactinomyces daqus	strain=H-18	GCA_000763315.1	1329516	1329516	type	True	76.9395	84	916	95	below_threshold
Laceyella sacchari	strain=DSM 43356	GCA_004343255.1	37482	37482	type	True	76.6401	78	916	95	below_threshold
Lihuaxuella thermophila	strain=DSM 46701	GCA_900110165.1	1173111	1173111	type	True	76.5713	119	916	95	below_threshold
Planifilum fimeticola	strain=DSM 44946	GCA_003001905.1	201975	201975	type	True	76.54	99	916	95	below_threshold
Marinithermofilum abyssi	strain=CGMCC 1.15179	GCA_014641195.1	1571185	1571185	type	True	76.4716	70	916	95	below_threshold
Planifilum fulgidum	strain=DSM 44945	GCA_900113175.1	201973	201973	type	True	76.3834	108	916	95	below_threshold
Melghirimyces profundicolus	strain=DSM 45787	GCA_003054245.1	1242148	1242148	type	True	76.2811	73	916	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:38:15,652] [INFO] DFAST Taxonomy check result was written to GCF_003856495.1_ASM385649v1_genomic.fna/tc_result.tsv
[2024-01-24 14:38:15,652] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:38:15,653] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:38:15,653] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5d0f3057-3361-4aa7-abc3-18660b2b433c/dqc_reference/checkm_data
[2024-01-24 14:38:15,655] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:38:15,691] [INFO] Task started: CheckM
[2024-01-24 14:38:15,691] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003856495.1_ASM385649v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003856495.1_ASM385649v1_genomic.fna/checkm_input GCF_003856495.1_ASM385649v1_genomic.fna/checkm_result
[2024-01-24 14:39:15,403] [INFO] Task succeeded: CheckM
[2024-01-24 14:39:15,405] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:39:15,434] [INFO] ===== Completeness check finished =====
[2024-01-24 14:39:15,434] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:39:15,434] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003856495.1_ASM385649v1_genomic.fna/markers.fasta)
[2024-01-24 14:39:15,435] [INFO] Task started: Blastn
[2024-01-24 14:39:15,435] [INFO] Running command: blastn -query GCF_003856495.1_ASM385649v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d0f3057-3361-4aa7-abc3-18660b2b433c/dqc_reference/reference_markers_gtdb.fasta -out GCF_003856495.1_ASM385649v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:16,332] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:16,338] [INFO] Selected 23 target genomes.
[2024-01-24 14:39:16,338] [INFO] Target genome list was writen to GCF_003856495.1_ASM385649v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:39:16,356] [INFO] Task started: fastANI
[2024-01-24 14:39:16,357] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfa42dd4-1f56-481e-8804-06e1bdc919ab/GCF_003856495.1_ASM385649v1_genomic.fna.gz --refList GCF_003856495.1_ASM385649v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003856495.1_ASM385649v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:39:30,775] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:30,784] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:39:30,785] [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_003856495.1	s__Staphylospora marina	100.0	916	916	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__Thermoactinomycetaceae;g__Staphylospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018326425.1	s__Polycladomyces abyssicola	77.8095	81	916	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_000763315.1	s__Thermoactinomyces_A daqus	76.9395	84	916	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__Thermoactinomycetaceae;g__Thermoactinomyces_A	95.0	99.52	99.22	0.92	0.88	5	-
GCF_004343255.1	s__Laceyella sacchari	76.6641	79	916	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__Thermoactinomycetaceae;g__Laceyella	95.237	96.84	96.83	0.94	0.94	3	-
GCF_900110165.1	s__Lihuaxuella thermophila	76.5587	121	916	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__Thermoactinomycetaceae;g__Lihuaxuella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003001905.1	s__Planifilum fimeticola	76.54	99	916	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__DSM-44946;g__Planifilum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641195.1	s__Marinithermofilum abyssi	76.4716	70	916	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__DSM-45169;g__Marinithermofilum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113175.1	s__Planifilum fulgidum	76.3834	108	916	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_003054245.1	s__Melghirimyces profundicolus	76.2811	73	916	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__DSM-45169;g__Melghirimyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:39:30,787] [INFO] GTDB search result was written to GCF_003856495.1_ASM385649v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:39:30,787] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:39:30,791] [INFO] DFAST_QC result json was written to GCF_003856495.1_ASM385649v1_genomic.fna/dqc_result.json
[2024-01-24 14:39:30,791] [INFO] DFAST_QC completed!
[2024-01-24 14:39:30,792] [INFO] Total running time: 0h1m43s