[2024-01-24 13:12:38,899] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:38,903] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:38,904] [INFO] DQC Reference Directory: /var/lib/cwl/stg2ff03066-8ee3-4c0e-8c62-5b06c5073801/dqc_reference
[2024-01-24 13:12:40,246] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:40,247] [INFO] Task started: Prodigal
[2024-01-24 13:12:40,247] [INFO] Running command: gunzip -c /var/lib/cwl/stgdeb534e9-9764-4738-b9de-f0286ad890b3/GCF_000520975.1_of_Aquimarina_megaterium_genomic.fna.gz | prodigal -d GCF_000520975.1_of_Aquimarina_megaterium_genomic.fna/cds.fna -a GCF_000520975.1_of_Aquimarina_megaterium_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:12:59,297] [INFO] Task succeeded: Prodigal
[2024-01-24 13:12:59,297] [INFO] Task started: HMMsearch
[2024-01-24 13:12:59,297] [INFO] Running command: hmmsearch --tblout GCF_000520975.1_of_Aquimarina_megaterium_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2ff03066-8ee3-4c0e-8c62-5b06c5073801/dqc_reference/reference_markers.hmm GCF_000520975.1_of_Aquimarina_megaterium_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:12:59,721] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:12:59,722] [INFO] Found 6/6 markers.
[2024-01-24 13:12:59,771] [INFO] Query marker FASTA was written to GCF_000520975.1_of_Aquimarina_megaterium_genomic.fna/markers.fasta
[2024-01-24 13:12:59,771] [INFO] Task started: Blastn
[2024-01-24 13:12:59,771] [INFO] Running command: blastn -query GCF_000520975.1_of_Aquimarina_megaterium_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ff03066-8ee3-4c0e-8c62-5b06c5073801/dqc_reference/reference_markers.fasta -out GCF_000520975.1_of_Aquimarina_megaterium_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:00,449] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:00,452] [INFO] Selected 13 target genomes.
[2024-01-24 13:13:00,453] [INFO] Target genome list was writen to GCF_000520975.1_of_Aquimarina_megaterium_genomic.fna/target_genomes.txt
[2024-01-24 13:13:00,460] [INFO] Task started: fastANI
[2024-01-24 13:13:00,460] [INFO] Running command: fastANI --query /var/lib/cwl/stgdeb534e9-9764-4738-b9de-f0286ad890b3/GCF_000520975.1_of_Aquimarina_megaterium_genomic.fna.gz --refList GCF_000520975.1_of_Aquimarina_megaterium_genomic.fna/target_genomes.txt --output GCF_000520975.1_of_Aquimarina_megaterium_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:12,806] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:12,806] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2ff03066-8ee3-4c0e-8c62-5b06c5073801/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:12,807] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2ff03066-8ee3-4c0e-8c62-5b06c5073801/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:12,823] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:12,823] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:12,823] [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
Aquimarina megaterium	strain=XH134	GCA_000520975.1	1443666	1443666	type	True	100.0	2010	2014	95	conclusive
Aquimarina atlantica	strain=22II-S11-z7	GCA_000626715.1	1317122	1317122	type	True	92.2234	1631	2014	95	below_threshold
Aquimarina macrocephali	strain=JAMB N27	GCA_000520995.1	666563	666563	type	True	89.5611	1521	2014	95	below_threshold
Aquimarina sediminis	strain=w01	GCA_002895435.1	2070536	2070536	type	True	80.3643	928	2014	95	below_threshold
Aquimarina longa	strain=SW024	GCA_001401755.1	1080221	1080221	type	True	80.1264	834	2014	95	below_threshold
Aquimarina muelleri	strain=DSM 19832	GCA_000430665.1	279356	279356	type	True	80.0279	809	2014	95	below_threshold
Aquimarina aggregata	strain=RZW4-3-2	GCA_001632745.1	1642818	1642818	type	True	78.9636	654	2014	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	76.3177	110	2014	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	76.1832	128	2014	95	below_threshold
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	76.0762	122	2014	95	below_threshold
Flavobacterium celericrescens	strain=TWA-26	GCA_011392075.1	2709780	2709780	type	True	75.9542	76	2014	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:12,825] [INFO] DFAST Taxonomy check result was written to GCF_000520975.1_of_Aquimarina_megaterium_genomic.fna/tc_result.tsv
[2024-01-24 13:13:12,825] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:12,825] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:12,825] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2ff03066-8ee3-4c0e-8c62-5b06c5073801/dqc_reference/checkm_data
[2024-01-24 13:13:12,826] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:12,884] [INFO] Task started: CheckM
[2024-01-24 13:13:12,885] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000520975.1_of_Aquimarina_megaterium_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000520975.1_of_Aquimarina_megaterium_genomic.fna/checkm_input GCF_000520975.1_of_Aquimarina_megaterium_genomic.fna/checkm_result
[2024-01-24 13:14:08,089] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:08,090] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:08,113] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:08,113] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:08,114] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000520975.1_of_Aquimarina_megaterium_genomic.fna/markers.fasta)
[2024-01-24 13:14:08,114] [INFO] Task started: Blastn
[2024-01-24 13:14:08,114] [INFO] Running command: blastn -query GCF_000520975.1_of_Aquimarina_megaterium_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ff03066-8ee3-4c0e-8c62-5b06c5073801/dqc_reference/reference_markers_gtdb.fasta -out GCF_000520975.1_of_Aquimarina_megaterium_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:09,026] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:09,030] [INFO] Selected 6 target genomes.
[2024-01-24 13:14:09,030] [INFO] Target genome list was writen to GCF_000520975.1_of_Aquimarina_megaterium_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:09,036] [INFO] Task started: fastANI
[2024-01-24 13:14:09,036] [INFO] Running command: fastANI --query /var/lib/cwl/stgdeb534e9-9764-4738-b9de-f0286ad890b3/GCF_000520975.1_of_Aquimarina_megaterium_genomic.fna.gz --refList GCF_000520975.1_of_Aquimarina_megaterium_genomic.fna/target_genomes_gtdb.txt --output GCF_000520975.1_of_Aquimarina_megaterium_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:18,048] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:18,060] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:18,060] [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_000520975.1	s__Aquimarina megaterium	100.0	2010	2014	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	98.79	98.77	0.92	0.92	4	conclusive
GCF_900312745.1	s__Aquimarina sp900312745	94.6429	1679	2014	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	95.61	95.54	0.91	0.91	4	-
GCF_000626715.1	s__Aquimarina atlantica	92.2152	1632	2014	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900299525.1	s__Aquimarina sp900299525	90.067	1672	2014	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000520995.1	s__Aquimarina macrocephali	89.5558	1522	2014	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002846555.1	s__Aquimarina sp002846555	87.6478	1334	2014	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:18,061] [INFO] GTDB search result was written to GCF_000520975.1_of_Aquimarina_megaterium_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:18,062] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:18,065] [INFO] DFAST_QC result json was written to GCF_000520975.1_of_Aquimarina_megaterium_genomic.fna/dqc_result.json
[2024-01-24 13:14:18,065] [INFO] DFAST_QC completed!
[2024-01-24 13:14:18,065] [INFO] Total running time: 0h1m39s