[2024-01-25 20:21:05,588] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:21:05,600] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:21:05,600] [INFO] DQC Reference Directory: /var/lib/cwl/stg249a3f19-2db2-410f-8e30-05b6098d8e6c/dqc_reference
[2024-01-25 20:21:06,780] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:21:06,781] [INFO] Task started: Prodigal
[2024-01-25 20:21:06,781] [INFO] Running command: gunzip -c /var/lib/cwl/stg1e25b1ce-1570-4aa6-800f-ad5de1d113eb/GCF_000014145.1_ASM1414v1_genomic.fna.gz | prodigal -d GCF_000014145.1_ASM1414v1_genomic.fna/cds.fna -a GCF_000014145.1_ASM1414v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:21:22,250] [INFO] Task succeeded: Prodigal
[2024-01-25 20:21:22,251] [INFO] Task started: HMMsearch
[2024-01-25 20:21:22,251] [INFO] Running command: hmmsearch --tblout GCF_000014145.1_ASM1414v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg249a3f19-2db2-410f-8e30-05b6098d8e6c/dqc_reference/reference_markers.hmm GCF_000014145.1_ASM1414v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:21:22,499] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:21:22,500] [INFO] Found 6/6 markers.
[2024-01-25 20:21:22,536] [INFO] Query marker FASTA was written to GCF_000014145.1_ASM1414v1_genomic.fna/markers.fasta
[2024-01-25 20:21:22,536] [INFO] Task started: Blastn
[2024-01-25 20:21:22,536] [INFO] Running command: blastn -query GCF_000014145.1_ASM1414v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg249a3f19-2db2-410f-8e30-05b6098d8e6c/dqc_reference/reference_markers.fasta -out GCF_000014145.1_ASM1414v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:21:23,078] [INFO] Task succeeded: Blastn
[2024-01-25 20:21:23,082] [INFO] Selected 20 target genomes.
[2024-01-25 20:21:23,083] [INFO] Target genome list was writen to GCF_000014145.1_ASM1414v1_genomic.fna/target_genomes.txt
[2024-01-25 20:21:23,095] [INFO] Task started: fastANI
[2024-01-25 20:21:23,095] [INFO] Running command: fastANI --query /var/lib/cwl/stg1e25b1ce-1570-4aa6-800f-ad5de1d113eb/GCF_000014145.1_ASM1414v1_genomic.fna.gz --refList GCF_000014145.1_ASM1414v1_genomic.fna/target_genomes.txt --output GCF_000014145.1_ASM1414v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:21:39,365] [INFO] Task succeeded: fastANI
[2024-01-25 20:21:39,365] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg249a3f19-2db2-410f-8e30-05b6098d8e6c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:21:39,365] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg249a3f19-2db2-410f-8e30-05b6098d8e6c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:21:39,370] [INFO] Found 3 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:21:39,370] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:21:39,370] [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
Cytophaga hutchinsonii	strain=ATCC 33406	GCA_000014145.1	985	985	type	True	100.0	1477	1477	95	conclusive
Cytophaga hutchinsonii	strain=DSM 1761	GCA_900119565.1	985	985	type	True	99.9691	1439	1477	95	conclusive
Cytophaga aurantiaca	strain=DSM 3654	GCA_000379725.1	29530	29530	type	True	80.378	651	1477	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:21:39,371] [INFO] DFAST Taxonomy check result was written to GCF_000014145.1_ASM1414v1_genomic.fna/tc_result.tsv
[2024-01-25 20:21:39,372] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:21:39,372] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:21:39,372] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg249a3f19-2db2-410f-8e30-05b6098d8e6c/dqc_reference/checkm_data
[2024-01-25 20:21:39,373] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:21:39,415] [INFO] Task started: CheckM
[2024-01-25 20:21:39,415] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000014145.1_ASM1414v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000014145.1_ASM1414v1_genomic.fna/checkm_input GCF_000014145.1_ASM1414v1_genomic.fna/checkm_result
[2024-01-25 20:22:25,557] [INFO] Task succeeded: CheckM
[2024-01-25 20:22:25,560] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:22:25,585] [INFO] ===== Completeness check finished =====
[2024-01-25 20:22:25,585] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:22:25,586] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000014145.1_ASM1414v1_genomic.fna/markers.fasta)
[2024-01-25 20:22:25,586] [INFO] Task started: Blastn
[2024-01-25 20:22:25,587] [INFO] Running command: blastn -query GCF_000014145.1_ASM1414v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg249a3f19-2db2-410f-8e30-05b6098d8e6c/dqc_reference/reference_markers_gtdb.fasta -out GCF_000014145.1_ASM1414v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:22:26,321] [INFO] Task succeeded: Blastn
[2024-01-25 20:22:26,324] [INFO] Selected 23 target genomes.
[2024-01-25 20:22:26,324] [INFO] Target genome list was writen to GCF_000014145.1_ASM1414v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:22:26,342] [INFO] Task started: fastANI
[2024-01-25 20:22:26,342] [INFO] Running command: fastANI --query /var/lib/cwl/stg1e25b1ce-1570-4aa6-800f-ad5de1d113eb/GCF_000014145.1_ASM1414v1_genomic.fna.gz --refList GCF_000014145.1_ASM1414v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000014145.1_ASM1414v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:22:44,608] [INFO] Task succeeded: fastANI
[2024-01-25 20:22:44,613] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:22:44,613] [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_000014145.1	s__Cytophaga hutchinsonii	100.0	1477	1477	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cytophagaceae;g__Cytophaga	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_000379725.1	s__Cytophaga aurantiaca	80.3832	651	1477	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cytophagaceae;g__Cytophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000775915.1	s__Sporocytophaga myxococcoides_A	75.526	65	1477	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cytophagaceae;g__Sporocytophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017745095.1	s__Sporocytophaga sp017745095	75.3413	56	1477	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cytophagaceae;g__Sporocytophaga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:22:44,614] [INFO] GTDB search result was written to GCF_000014145.1_ASM1414v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:22:44,615] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:22:44,616] [INFO] DFAST_QC result json was written to GCF_000014145.1_ASM1414v1_genomic.fna/dqc_result.json
[2024-01-25 20:22:44,617] [INFO] DFAST_QC completed!
[2024-01-25 20:22:44,617] [INFO] Total running time: 0h1m39s