[2024-01-24 10:48:09,871] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:48:09,875] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:48:09,875] [INFO] DQC Reference Directory: /var/lib/cwl/stge36d6dd4-fef0-44d3-a2e9-2f0c8750b4a8/dqc_reference
[2024-01-24 10:48:23,955] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:48:23,957] [INFO] Task started: Prodigal
[2024-01-24 10:48:23,957] [INFO] Running command: gunzip -c /var/lib/cwl/stge6fba71d-9573-4318-9bae-b51ef1c6f625/GCF_008014675.1_ASM801467v1_genomic.fna.gz | prodigal -d GCF_008014675.1_ASM801467v1_genomic.fna/cds.fna -a GCF_008014675.1_ASM801467v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:48:52,525] [INFO] Task succeeded: Prodigal
[2024-01-24 10:48:52,525] [INFO] Task started: HMMsearch
[2024-01-24 10:48:52,525] [INFO] Running command: hmmsearch --tblout GCF_008014675.1_ASM801467v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge36d6dd4-fef0-44d3-a2e9-2f0c8750b4a8/dqc_reference/reference_markers.hmm GCF_008014675.1_ASM801467v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:48:52,888] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:48:52,889] [INFO] Found 6/6 markers.
[2024-01-24 10:48:52,948] [INFO] Query marker FASTA was written to GCF_008014675.1_ASM801467v1_genomic.fna/markers.fasta
[2024-01-24 10:48:52,949] [INFO] Task started: Blastn
[2024-01-24 10:48:52,949] [INFO] Running command: blastn -query GCF_008014675.1_ASM801467v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge36d6dd4-fef0-44d3-a2e9-2f0c8750b4a8/dqc_reference/reference_markers.fasta -out GCF_008014675.1_ASM801467v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:53,585] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:53,590] [INFO] Selected 10 target genomes.
[2024-01-24 10:48:53,590] [INFO] Target genome list was writen to GCF_008014675.1_ASM801467v1_genomic.fna/target_genomes.txt
[2024-01-24 10:48:53,596] [INFO] Task started: fastANI
[2024-01-24 10:48:53,596] [INFO] Running command: fastANI --query /var/lib/cwl/stge6fba71d-9573-4318-9bae-b51ef1c6f625/GCF_008014675.1_ASM801467v1_genomic.fna.gz --refList GCF_008014675.1_ASM801467v1_genomic.fna/target_genomes.txt --output GCF_008014675.1_ASM801467v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:49:07,397] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:07,398] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge36d6dd4-fef0-44d3-a2e9-2f0c8750b4a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:49:07,399] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge36d6dd4-fef0-44d3-a2e9-2f0c8750b4a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:49:07,412] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:49:07,413] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:49:07,413] [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
Neolewinella aurantiaca	strain=SSH13	GCA_008014675.1	2602767	2602767	type	True	100.0	1941	1944	95	conclusive
Neolewinella agarilytica	strain=DSM 24740	GCA_900110645.1	478744	478744	type	True	78.0747	361	1944	95	below_threshold
Neolewinella persica	strain=DSM 23188	GCA_000373105.1	70998	70998	type	True	77.5985	376	1944	95	below_threshold
Neolewinella lacunae	strain=KCTC 42187	GCA_014349155.1	1517758	1517758	type	True	76.7647	288	1944	95	below_threshold
Neolewinella marina	strain=MKG-38	GCA_002631205.1	438751	438751	type	True	76.5689	179	1944	95	below_threshold
Neolewinella antarctica	strain=DSM 105096	GCA_011927835.1	442734	442734	type	True	76.2395	183	1944	95	below_threshold
Neolewinella xylanilytica	strain=DSM 29526	GCA_002934605.1	1514080	1514080	type	True	76.2086	128	1944	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:49:07,414] [INFO] DFAST Taxonomy check result was written to GCF_008014675.1_ASM801467v1_genomic.fna/tc_result.tsv
[2024-01-24 10:49:07,415] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:49:07,415] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:49:07,415] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge36d6dd4-fef0-44d3-a2e9-2f0c8750b4a8/dqc_reference/checkm_data
[2024-01-24 10:49:07,416] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:49:07,472] [INFO] Task started: CheckM
[2024-01-24 10:49:07,472] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008014675.1_ASM801467v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008014675.1_ASM801467v1_genomic.fna/checkm_input GCF_008014675.1_ASM801467v1_genomic.fna/checkm_result
[2024-01-24 10:50:28,366] [INFO] Task succeeded: CheckM
[2024-01-24 10:50:28,367] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:50:28,390] [INFO] ===== Completeness check finished =====
[2024-01-24 10:50:28,390] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:50:28,391] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008014675.1_ASM801467v1_genomic.fna/markers.fasta)
[2024-01-24 10:50:28,391] [INFO] Task started: Blastn
[2024-01-24 10:50:28,391] [INFO] Running command: blastn -query GCF_008014675.1_ASM801467v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge36d6dd4-fef0-44d3-a2e9-2f0c8750b4a8/dqc_reference/reference_markers_gtdb.fasta -out GCF_008014675.1_ASM801467v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:50:29,183] [INFO] Task succeeded: Blastn
[2024-01-24 10:50:29,187] [INFO] Selected 14 target genomes.
[2024-01-24 10:50:29,188] [INFO] Target genome list was writen to GCF_008014675.1_ASM801467v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:50:29,204] [INFO] Task started: fastANI
[2024-01-24 10:50:29,204] [INFO] Running command: fastANI --query /var/lib/cwl/stge6fba71d-9573-4318-9bae-b51ef1c6f625/GCF_008014675.1_ASM801467v1_genomic.fna.gz --refList GCF_008014675.1_ASM801467v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008014675.1_ASM801467v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:50:44,044] [INFO] Task succeeded: fastANI
[2024-01-24 10:50:44,055] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:50:44,056] [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_008014675.1	s__Lewinella_A aurantiaca	100.0	1941	1944	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900110645.1	s__Lewinella_A agarilytica	78.0747	361	1944	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000373105.1	s__Lewinella_A persica	77.6085	374	1944	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001625015.1	s__Lewinella_A sp001625015	76.8763	211	1944	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014349155.1	s__Lewinella_A lacunae	76.8222	289	1944	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002631205.1	s__Lewinella_A marina	76.5689	179	1944	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003390935.1	s__Lewinella_A sp003390935	76.2611	156	1944	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011927835.1	s__Lewinella_A antarctica	76.2488	182	1944	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:50:44,058] [INFO] GTDB search result was written to GCF_008014675.1_ASM801467v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:50:44,058] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:50:44,061] [INFO] DFAST_QC result json was written to GCF_008014675.1_ASM801467v1_genomic.fna/dqc_result.json
[2024-01-24 10:50:44,062] [INFO] DFAST_QC completed!
[2024-01-24 10:50:44,062] [INFO] Total running time: 0h2m34s