[2024-01-24 12:21:40,324] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:40,327] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:40,327] [INFO] DQC Reference Directory: /var/lib/cwl/stg070b3d25-2ffe-4b44-9dac-2043d30a11e9/dqc_reference
[2024-01-24 12:21:42,918] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:42,919] [INFO] Task started: Prodigal
[2024-01-24 12:21:42,920] [INFO] Running command: gunzip -c /var/lib/cwl/stg609ad39e-4d5c-4672-95aa-8937fb93a813/GCF_000371925.1_ASM37192v1_genomic.fna.gz | prodigal -d GCF_000371925.1_ASM37192v1_genomic.fna/cds.fna -a GCF_000371925.1_ASM37192v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:21:52,302] [INFO] Task succeeded: Prodigal
[2024-01-24 12:21:52,303] [INFO] Task started: HMMsearch
[2024-01-24 12:21:52,303] [INFO] Running command: hmmsearch --tblout GCF_000371925.1_ASM37192v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg070b3d25-2ffe-4b44-9dac-2043d30a11e9/dqc_reference/reference_markers.hmm GCF_000371925.1_ASM37192v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:21:52,681] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:21:52,682] [INFO] Found 6/6 markers.
[2024-01-24 12:21:52,718] [INFO] Query marker FASTA was written to GCF_000371925.1_ASM37192v1_genomic.fna/markers.fasta
[2024-01-24 12:21:52,718] [INFO] Task started: Blastn
[2024-01-24 12:21:52,718] [INFO] Running command: blastn -query GCF_000371925.1_ASM37192v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg070b3d25-2ffe-4b44-9dac-2043d30a11e9/dqc_reference/reference_markers.fasta -out GCF_000371925.1_ASM37192v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:21:53,313] [INFO] Task succeeded: Blastn
[2024-01-24 12:21:53,316] [INFO] Selected 24 target genomes.
[2024-01-24 12:21:53,316] [INFO] Target genome list was writen to GCF_000371925.1_ASM37192v1_genomic.fna/target_genomes.txt
[2024-01-24 12:21:53,353] [INFO] Task started: fastANI
[2024-01-24 12:21:53,353] [INFO] Running command: fastANI --query /var/lib/cwl/stg609ad39e-4d5c-4672-95aa-8937fb93a813/GCF_000371925.1_ASM37192v1_genomic.fna.gz --refList GCF_000371925.1_ASM37192v1_genomic.fna/target_genomes.txt --output GCF_000371925.1_ASM37192v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:08,957] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:08,957] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg070b3d25-2ffe-4b44-9dac-2043d30a11e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:08,958] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg070b3d25-2ffe-4b44-9dac-2043d30a11e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:08,964] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:22:08,965] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:08,965] [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
Thiolinea disciformis	strain=DSM 14473	GCA_000371925.1	125614	125614	type	True	100.0	1270	1273	95	conclusive
Thiothrix litoralis	strain=AS	GCA_017901135.1	2891210	2891210	type	True	77.4181	57	1273	95	below_threshold
Thiothrix eikelboomii	strain=ATCC 49788	GCA_900167255.1	92487	92487	type	True	77.2602	205	1273	95	below_threshold
Thiothrix winogradskyi	strain=CT3	GCA_021650935.1	96472	96472	type	True	77.188	52	1273	95	below_threshold
Thiothrix fructosivorans	strain=ATCC 49748	GCA_017349355.1	111770	111770	type	True	76.3744	67	1273	95	below_threshold
Thiofilum flexile	strain=DSM 14609	GCA_000380185.1	125627	125627	type	True	76.147	101	1273	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:08,975] [INFO] DFAST Taxonomy check result was written to GCF_000371925.1_ASM37192v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:08,976] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:08,977] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:08,977] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg070b3d25-2ffe-4b44-9dac-2043d30a11e9/dqc_reference/checkm_data
[2024-01-24 12:22:08,978] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:09,031] [INFO] Task started: CheckM
[2024-01-24 12:22:09,032] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000371925.1_ASM37192v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000371925.1_ASM37192v1_genomic.fna/checkm_input GCF_000371925.1_ASM37192v1_genomic.fna/checkm_result
[2024-01-24 12:22:43,003] [INFO] Task succeeded: CheckM
[2024-01-24 12:22:43,004] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:22:43,024] [INFO] ===== Completeness check finished =====
[2024-01-24 12:22:43,024] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:22:43,025] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000371925.1_ASM37192v1_genomic.fna/markers.fasta)
[2024-01-24 12:22:43,025] [INFO] Task started: Blastn
[2024-01-24 12:22:43,025] [INFO] Running command: blastn -query GCF_000371925.1_ASM37192v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg070b3d25-2ffe-4b44-9dac-2043d30a11e9/dqc_reference/reference_markers_gtdb.fasta -out GCF_000371925.1_ASM37192v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:43,861] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:43,864] [INFO] Selected 20 target genomes.
[2024-01-24 12:22:43,865] [INFO] Target genome list was writen to GCF_000371925.1_ASM37192v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:22:44,150] [INFO] Task started: fastANI
[2024-01-24 12:22:44,150] [INFO] Running command: fastANI --query /var/lib/cwl/stg609ad39e-4d5c-4672-95aa-8937fb93a813/GCF_000371925.1_ASM37192v1_genomic.fna.gz --refList GCF_000371925.1_ASM37192v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000371925.1_ASM37192v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:22:56,125] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:56,133] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:22:56,134] [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_000371925.1	s__Thiolinea disciformis	100.0	1270	1273	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiotrichales;f__Thiotrichaceae;g__Thiolinea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_008015155.1	s__Thiolinea sp008015155	78.1153	222	1273	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiotrichales;f__Thiotrichaceae;g__Thiolinea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167255.1	s__Thiolinea eikelboomii	77.328	206	1273	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiotrichales;f__Thiotrichaceae;g__Thiolinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016711335.1	s__Thiofilum sp016711335	76.6544	140	1273	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiotrichales;f__Thiotrichaceae;g__Thiofilum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000380185.1	s__Thiofilum flexile	76.1644	100	1273	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiotrichales;f__Thiotrichaceae;g__Thiofilum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002747435.1	s__Thiolinea sp002747435	76.0424	79	1273	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiotrichales;f__Thiotrichaceae;g__Thiolinea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:22:56,135] [INFO] GTDB search result was written to GCF_000371925.1_ASM37192v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:22:56,136] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:22:56,142] [INFO] DFAST_QC result json was written to GCF_000371925.1_ASM37192v1_genomic.fna/dqc_result.json
[2024-01-24 12:22:56,142] [INFO] DFAST_QC completed!
[2024-01-24 12:22:56,143] [INFO] Total running time: 0h1m16s