[2024-01-24 13:54:04,016] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:54:04,022] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:54:04,022] [INFO] DQC Reference Directory: /var/lib/cwl/stge841b8f4-6415-4900-8fa3-60f95ebd1daf/dqc_reference
[2024-01-24 13:54:05,531] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:54:05,532] [INFO] Task started: Prodigal
[2024-01-24 13:54:05,533] [INFO] Running command: gunzip -c /var/lib/cwl/stgc952706a-7cd8-42e9-aed3-7756bfb6cfe5/GCF_000196895.1_ASM19689v1_genomic.fna.gz | prodigal -d GCF_000196895.1_ASM19689v1_genomic.fna/cds.fna -a GCF_000196895.1_ASM19689v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:54:24,959] [INFO] Task succeeded: Prodigal
[2024-01-24 13:54:24,959] [INFO] Task started: HMMsearch
[2024-01-24 13:54:24,960] [INFO] Running command: hmmsearch --tblout GCF_000196895.1_ASM19689v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge841b8f4-6415-4900-8fa3-60f95ebd1daf/dqc_reference/reference_markers.hmm GCF_000196895.1_ASM19689v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:54:25,327] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:54:25,329] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgc952706a-7cd8-42e9-aed3-7756bfb6cfe5/GCF_000196895.1_ASM19689v1_genomic.fna.gz]
[2024-01-24 13:54:25,375] [INFO] Query marker FASTA was written to GCF_000196895.1_ASM19689v1_genomic.fna/markers.fasta
[2024-01-24 13:54:25,375] [INFO] Task started: Blastn
[2024-01-24 13:54:25,375] [INFO] Running command: blastn -query GCF_000196895.1_ASM19689v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge841b8f4-6415-4900-8fa3-60f95ebd1daf/dqc_reference/reference_markers.fasta -out GCF_000196895.1_ASM19689v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:54:25,984] [INFO] Task succeeded: Blastn
[2024-01-24 13:54:25,987] [INFO] Selected 6 target genomes.
[2024-01-24 13:54:25,988] [INFO] Target genome list was writen to GCF_000196895.1_ASM19689v1_genomic.fna/target_genomes.txt
[2024-01-24 13:54:25,998] [INFO] Task started: fastANI
[2024-01-24 13:54:25,998] [INFO] Running command: fastANI --query /var/lib/cwl/stgc952706a-7cd8-42e9-aed3-7756bfb6cfe5/GCF_000196895.1_ASM19689v1_genomic.fna.gz --refList GCF_000196895.1_ASM19689v1_genomic.fna/target_genomes.txt --output GCF_000196895.1_ASM19689v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:54:32,704] [INFO] Task succeeded: fastANI
[2024-01-24 13:54:32,704] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge841b8f4-6415-4900-8fa3-60f95ebd1daf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:54:32,705] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge841b8f4-6415-4900-8fa3-60f95ebd1daf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:54:32,713] [INFO] Found 6 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:54:32,713] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:54:32,713] [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
Halalkalicoccus jeotgali	strain=B3	GCA_000196895.1	413810	413810	type	True	100.0	1215	1229	95	conclusive
Halalkalicoccus jeotgali	strain=B3	GCA_000485535.1	413810	413810	type	True	99.9837	1193	1229	95	conclusive
Halalkalicoccus jeotgali	strain=B3	GCA_000337255.1	413810	413810	type	True	99.9578	1174	1229	95	conclusive
Halalkalicoccus paucihalophilus	strain=DSM 24557	GCA_001593955.1	1008153	1008153	type	True	85.8876	882	1229	95	below_threshold
Halalkalicoccus subterraneus	strain=GSM28	GCA_003697815.1	2675002	2675002	type	True	84.9165	758	1229	95	below_threshold
Halosimplex rubrum	strain=R27	GCA_013415885.1	869889	869889	type	True	77.1131	347	1229	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:54:32,719] [INFO] DFAST Taxonomy check result was written to GCF_000196895.1_ASM19689v1_genomic.fna/tc_result.tsv
[2024-01-24 13:54:32,720] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:54:32,720] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:54:32,720] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge841b8f4-6415-4900-8fa3-60f95ebd1daf/dqc_reference/checkm_data
[2024-01-24 13:54:32,722] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:54:32,769] [INFO] Task started: CheckM
[2024-01-24 13:54:32,770] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000196895.1_ASM19689v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000196895.1_ASM19689v1_genomic.fna/checkm_input GCF_000196895.1_ASM19689v1_genomic.fna/checkm_result
[2024-01-24 13:55:24,097] [INFO] Task succeeded: CheckM
[2024-01-24 13:55:24,098] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:55:24,117] [INFO] ===== Completeness check finished =====
[2024-01-24 13:55:24,118] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:55:24,118] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000196895.1_ASM19689v1_genomic.fna/markers.fasta)
[2024-01-24 13:55:24,119] [INFO] Task started: Blastn
[2024-01-24 13:55:24,119] [INFO] Running command: blastn -query GCF_000196895.1_ASM19689v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge841b8f4-6415-4900-8fa3-60f95ebd1daf/dqc_reference/reference_markers_gtdb.fasta -out GCF_000196895.1_ASM19689v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:24,664] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:24,668] [INFO] Selected 9 target genomes.
[2024-01-24 13:55:24,668] [INFO] Target genome list was writen to GCF_000196895.1_ASM19689v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:55:24,686] [INFO] Task started: fastANI
[2024-01-24 13:55:24,686] [INFO] Running command: fastANI --query /var/lib/cwl/stgc952706a-7cd8-42e9-aed3-7756bfb6cfe5/GCF_000196895.1_ASM19689v1_genomic.fna.gz --refList GCF_000196895.1_ASM19689v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000196895.1_ASM19689v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:55:31,351] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:31,363] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:55:31,364] [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_000196895.1	s__Halalkalicoccus jeotgali	100.0	1216	1229	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halalkalicoccaceae;g__Halalkalicoccus	95.0	99.99	99.98	1.00	1.00	3	conclusive
GCF_001593955.1	s__Halalkalicoccus paucihalophilus	85.8876	882	1229	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halalkalicoccaceae;g__Halalkalicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003697815.1	s__Halalkalicoccus subterraneus	84.9409	756	1229	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halalkalicoccaceae;g__Halalkalicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007129135.1	s__SKXI01 sp007129135	78.205	297	1229	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halalkalicoccaceae;g__SKXI01	95.0	99.24	99.24	0.85	0.85	2	-
GCA_007128515.1	s__SKXI01 sp007128515	78.1574	236	1229	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halalkalicoccaceae;g__SKXI01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003369835.1	s__Halorussus rarus	77.5487	354	1229	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Halorussus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013456555.1	s__Natrinema sp013456555	77.35	319	1229	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000337215.1	s__Natronolimnohabitans innermongolicus	77.3346	319	1229	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronolimnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647115.1	s__Halarchaeum rubridurum	76.8651	244	1229	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halobacteriaceae;g__Halarchaeum	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:55:31,365] [INFO] GTDB search result was written to GCF_000196895.1_ASM19689v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:55:31,366] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:55:31,369] [INFO] DFAST_QC result json was written to GCF_000196895.1_ASM19689v1_genomic.fna/dqc_result.json
[2024-01-24 13:55:31,369] [INFO] DFAST_QC completed!
[2024-01-24 13:55:31,369] [INFO] Total running time: 0h1m27s