[2024-01-24 15:18:27,599] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:27,600] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:27,601] [INFO] DQC Reference Directory: /var/lib/cwl/stgb0393833-4f70-481e-820b-e23cb237db5f/dqc_reference
[2024-01-24 15:18:28,878] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:28,879] [INFO] Task started: Prodigal
[2024-01-24 15:18:28,879] [INFO] Running command: gunzip -c /var/lib/cwl/stg59657b8c-b221-4b8c-b040-723df96fe17e/GCF_003205875.1_ASM320587v1_genomic.fna.gz | prodigal -d GCF_003205875.1_ASM320587v1_genomic.fna/cds.fna -a GCF_003205875.1_ASM320587v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:51,041] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:51,041] [INFO] Task started: HMMsearch
[2024-01-24 15:18:51,041] [INFO] Running command: hmmsearch --tblout GCF_003205875.1_ASM320587v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb0393833-4f70-481e-820b-e23cb237db5f/dqc_reference/reference_markers.hmm GCF_003205875.1_ASM320587v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:51,393] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:51,394] [INFO] Found 6/6 markers.
[2024-01-24 15:18:51,462] [INFO] Query marker FASTA was written to GCF_003205875.1_ASM320587v1_genomic.fna/markers.fasta
[2024-01-24 15:18:51,463] [INFO] Task started: Blastn
[2024-01-24 15:18:51,463] [INFO] Running command: blastn -query GCF_003205875.1_ASM320587v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0393833-4f70-481e-820b-e23cb237db5f/dqc_reference/reference_markers.fasta -out GCF_003205875.1_ASM320587v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:52,046] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:52,050] [INFO] Selected 12 target genomes.
[2024-01-24 15:18:52,050] [INFO] Target genome list was writen to GCF_003205875.1_ASM320587v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:52,057] [INFO] Task started: fastANI
[2024-01-24 15:18:52,057] [INFO] Running command: fastANI --query /var/lib/cwl/stg59657b8c-b221-4b8c-b040-723df96fe17e/GCF_003205875.1_ASM320587v1_genomic.fna.gz --refList GCF_003205875.1_ASM320587v1_genomic.fna/target_genomes.txt --output GCF_003205875.1_ASM320587v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:07,926] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:07,926] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb0393833-4f70-481e-820b-e23cb237db5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:07,927] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb0393833-4f70-481e-820b-e23cb237db5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:07,932] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:19:07,932] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:07,932] [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
Herpetosiphon llansteffanensis	strain=CA052B	GCA_003205875.1	2094568	2094568	type	True	100.0	1974	1975	95	conclusive
Herpetosiphon giganteus	strain=DSM 589	GCA_016907925.1	2029754	2029754	type	True	92.2172	1751	1975	95	below_threshold
Herpetosiphon geysericola	strain=DSM 7119	GCA_001306135.1	70996	70996	type	True	91.5191	1696	1975	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:07,934] [INFO] DFAST Taxonomy check result was written to GCF_003205875.1_ASM320587v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:07,935] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:07,935] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:07,935] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb0393833-4f70-481e-820b-e23cb237db5f/dqc_reference/checkm_data
[2024-01-24 15:19:07,937] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:08,003] [INFO] Task started: CheckM
[2024-01-24 15:19:08,003] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003205875.1_ASM320587v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003205875.1_ASM320587v1_genomic.fna/checkm_input GCF_003205875.1_ASM320587v1_genomic.fna/checkm_result
[2024-01-24 15:20:09,590] [INFO] Task succeeded: CheckM
[2024-01-24 15:20:09,592] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:20:09,615] [INFO] ===== Completeness check finished =====
[2024-01-24 15:20:09,615] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:20:09,616] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003205875.1_ASM320587v1_genomic.fna/markers.fasta)
[2024-01-24 15:20:09,616] [INFO] Task started: Blastn
[2024-01-24 15:20:09,616] [INFO] Running command: blastn -query GCF_003205875.1_ASM320587v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0393833-4f70-481e-820b-e23cb237db5f/dqc_reference/reference_markers_gtdb.fasta -out GCF_003205875.1_ASM320587v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:20:10,355] [INFO] Task succeeded: Blastn
[2024-01-24 15:20:10,359] [INFO] Selected 10 target genomes.
[2024-01-24 15:20:10,360] [INFO] Target genome list was writen to GCF_003205875.1_ASM320587v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:20:10,376] [INFO] Task started: fastANI
[2024-01-24 15:20:10,377] [INFO] Running command: fastANI --query /var/lib/cwl/stg59657b8c-b221-4b8c-b040-723df96fe17e/GCF_003205875.1_ASM320587v1_genomic.fna.gz --refList GCF_003205875.1_ASM320587v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003205875.1_ASM320587v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:20:25,099] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:25,111] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:20:25,111] [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_003205875.1	s__Herpetosiphon llansteffanensis	100.0	1974	1975	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Herpetosiphonaceae;g__Herpetosiphon	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016907925.1	s__Herpetosiphon giganteus	92.2072	1752	1975	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Herpetosiphonaceae;g__Herpetosiphon	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001306135.1	s__Herpetosiphon geysericola	91.5276	1695	1975	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Herpetosiphonaceae;g__Herpetosiphon	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000018565.1	s__Herpetosiphon aurantiacus	85.2467	1568	1975	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Herpetosiphonaceae;g__Herpetosiphon	95.0	99.99	99.99	1.00	1.00	2	-
GCA_013813565.1	s__JACCRK01 sp013813565	76.0112	99	1975	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Herpetosiphonaceae;g__JACCRK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013538855.1	s__OHK22 sp013538855	75.5575	81	1975	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Herpetosiphonaceae;g__OHK22	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:20:25,112] [INFO] GTDB search result was written to GCF_003205875.1_ASM320587v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:20:25,113] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:20:25,116] [INFO] DFAST_QC result json was written to GCF_003205875.1_ASM320587v1_genomic.fna/dqc_result.json
[2024-01-24 15:20:25,116] [INFO] DFAST_QC completed!
[2024-01-24 15:20:25,116] [INFO] Total running time: 0h1m58s