[2024-01-25 19:43:05,408] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:43:05,409] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:43:05,409] [INFO] DQC Reference Directory: /var/lib/cwl/stg24eb486a-0bfd-4d14-b03a-135b599e180f/dqc_reference
[2024-01-25 19:43:06,563] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:43:06,563] [INFO] Task started: Prodigal
[2024-01-25 19:43:06,564] [INFO] Running command: gunzip -c /var/lib/cwl/stg2af3feea-9178-4d6d-8154-61cbabc16f7b/GCF_013265585.1_ASM1326558v1_genomic.fna.gz | prodigal -d GCF_013265585.1_ASM1326558v1_genomic.fna/cds.fna -a GCF_013265585.1_ASM1326558v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:43:17,809] [INFO] Task succeeded: Prodigal
[2024-01-25 19:43:17,809] [INFO] Task started: HMMsearch
[2024-01-25 19:43:17,809] [INFO] Running command: hmmsearch --tblout GCF_013265585.1_ASM1326558v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg24eb486a-0bfd-4d14-b03a-135b599e180f/dqc_reference/reference_markers.hmm GCF_013265585.1_ASM1326558v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:43:18,006] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:43:18,007] [INFO] Found 6/6 markers.
[2024-01-25 19:43:18,033] [INFO] Query marker FASTA was written to GCF_013265585.1_ASM1326558v1_genomic.fna/markers.fasta
[2024-01-25 19:43:18,033] [INFO] Task started: Blastn
[2024-01-25 19:43:18,033] [INFO] Running command: blastn -query GCF_013265585.1_ASM1326558v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24eb486a-0bfd-4d14-b03a-135b599e180f/dqc_reference/reference_markers.fasta -out GCF_013265585.1_ASM1326558v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:43:18,573] [INFO] Task succeeded: Blastn
[2024-01-25 19:43:18,581] [INFO] Selected 16 target genomes.
[2024-01-25 19:43:18,581] [INFO] Target genome list was writen to GCF_013265585.1_ASM1326558v1_genomic.fna/target_genomes.txt
[2024-01-25 19:43:18,594] [INFO] Task started: fastANI
[2024-01-25 19:43:18,594] [INFO] Running command: fastANI --query /var/lib/cwl/stg2af3feea-9178-4d6d-8154-61cbabc16f7b/GCF_013265585.1_ASM1326558v1_genomic.fna.gz --refList GCF_013265585.1_ASM1326558v1_genomic.fna/target_genomes.txt --output GCF_013265585.1_ASM1326558v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:43:31,111] [INFO] Task succeeded: fastANI
[2024-01-25 19:43:31,111] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg24eb486a-0bfd-4d14-b03a-135b599e180f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:43:31,111] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg24eb486a-0bfd-4d14-b03a-135b599e180f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:43:31,118] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:43:31,119] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:43:31,119] [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
Kroppenstedtia pulmonis	strain=W9323	GCA_013265585.1	1380685	1380685	type	True	100.0	1114	1115	95	conclusive
Paludifilum halophilum	strain=DSM 102817	GCA_002245355.1	1642702	1642702	type	True	77.301	149	1115	95	below_threshold
Marinithermofilum abyssi	strain=CGMCC 1.15179	GCA_014641195.1	1571185	1571185	type	True	77.0331	85	1115	95	below_threshold
Desmospora activa	strain=DSM 45169	GCA_003046315.1	500615	500615	type	True	76.8928	100	1115	95	below_threshold
Melghirimyces algeriensis	strain=DSM 45474	GCA_900182565.1	910412	910412	type	True	76.8405	87	1115	95	below_threshold
Melghirimyces thermohalophilus	strain=DSM 45514	GCA_900102685.1	1236220	1236220	type	True	76.8309	92	1115	95	below_threshold
Melghirimyces profundicolus	strain=DSM 45787	GCA_003054245.1	1242148	1242148	type	True	76.7984	71	1115	95	below_threshold
Marininema halotolerans	strain=DSM 45789	GCA_900116235.1	1155944	1155944	type	True	76.6805	51	1115	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:43:31,120] [INFO] DFAST Taxonomy check result was written to GCF_013265585.1_ASM1326558v1_genomic.fna/tc_result.tsv
[2024-01-25 19:43:31,120] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:43:31,121] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:43:31,121] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg24eb486a-0bfd-4d14-b03a-135b599e180f/dqc_reference/checkm_data
[2024-01-25 19:43:31,122] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:43:31,154] [INFO] Task started: CheckM
[2024-01-25 19:43:31,154] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013265585.1_ASM1326558v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013265585.1_ASM1326558v1_genomic.fna/checkm_input GCF_013265585.1_ASM1326558v1_genomic.fna/checkm_result
[2024-01-25 19:44:06,553] [INFO] Task succeeded: CheckM
[2024-01-25 19:44:06,555] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:44:06,572] [INFO] ===== Completeness check finished =====
[2024-01-25 19:44:06,572] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:44:06,574] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013265585.1_ASM1326558v1_genomic.fna/markers.fasta)
[2024-01-25 19:44:06,574] [INFO] Task started: Blastn
[2024-01-25 19:44:06,574] [INFO] Running command: blastn -query GCF_013265585.1_ASM1326558v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24eb486a-0bfd-4d14-b03a-135b599e180f/dqc_reference/reference_markers_gtdb.fasta -out GCF_013265585.1_ASM1326558v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:44:07,331] [INFO] Task succeeded: Blastn
[2024-01-25 19:44:07,338] [INFO] Selected 17 target genomes.
[2024-01-25 19:44:07,338] [INFO] Target genome list was writen to GCF_013265585.1_ASM1326558v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:44:07,350] [INFO] Task started: fastANI
[2024-01-25 19:44:07,350] [INFO] Running command: fastANI --query /var/lib/cwl/stg2af3feea-9178-4d6d-8154-61cbabc16f7b/GCF_013265585.1_ASM1326558v1_genomic.fna.gz --refList GCF_013265585.1_ASM1326558v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013265585.1_ASM1326558v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:44:18,793] [INFO] Task succeeded: fastANI
[2024-01-25 19:44:18,799] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:44:18,799] [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_013265585.1	s__Kroppenstedtia_A pulmonis	100.0	1114	1115	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	conclusive
GCF_002245355.1	s__Paludifilum halophilum	77.301	149	1115	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__DSM-45169;g__Paludifilum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641195.1	s__Marinithermofilum abyssi	77.0021	86	1115	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_003046315.1	s__Desmospora activa	76.9178	99	1115	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	76.8663	86	1115	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_003054245.1	s__Melghirimyces profundicolus	76.8269	72	1115	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_900102685.1	s__Melghirimyces thermohalophilus	76.8051	92	1115	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_900116235.1	s__Marininema halotolerans	76.6805	51	1115	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__DSM-45169;g__Marininema	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:44:18,801] [INFO] GTDB search result was written to GCF_013265585.1_ASM1326558v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:44:18,801] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:44:18,805] [INFO] DFAST_QC result json was written to GCF_013265585.1_ASM1326558v1_genomic.fna/dqc_result.json
[2024-01-25 19:44:18,805] [INFO] DFAST_QC completed!
[2024-01-25 19:44:18,805] [INFO] Total running time: 0h1m13s