[2023-06-05 08:20:59,146] [INFO] DFAST_QC pipeline started.
[2023-06-05 08:20:59,149] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 08:20:59,150] [INFO] DQC Reference Directory: /var/lib/cwl/stgea380155-b405-4a3b-a2e0-707bba509fe6/dqc_reference
[2023-06-05 08:21:01,208] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 08:21:01,209] [INFO] Task started: Prodigal
[2023-06-05 08:21:01,209] [INFO] Running command: gunzip -c /var/lib/cwl/stg996d073b-916a-4c18-8668-ed020be078b8/GCA_902628965.1_AH-324-F03_genomic.fna.gz | prodigal -d GCA_902628965.1_AH-324-F03_genomic.fna/cds.fna -a GCA_902628965.1_AH-324-F03_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 08:21:04,540] [INFO] Task succeeded: Prodigal
[2023-06-05 08:21:04,540] [INFO] Task started: HMMsearch
[2023-06-05 08:21:04,540] [INFO] Running command: hmmsearch --tblout GCA_902628965.1_AH-324-F03_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea380155-b405-4a3b-a2e0-707bba509fe6/dqc_reference/reference_markers.hmm GCA_902628965.1_AH-324-F03_genomic.fna/protein.faa > /dev/null
[2023-06-05 08:21:04,759] [INFO] Task succeeded: HMMsearch
[2023-06-05 08:21:04,760] [INFO] Found 6/6 markers.
[2023-06-05 08:21:04,785] [INFO] Query marker FASTA was written to GCA_902628965.1_AH-324-F03_genomic.fna/markers.fasta
[2023-06-05 08:21:04,785] [INFO] Task started: Blastn
[2023-06-05 08:21:04,786] [INFO] Running command: blastn -query GCA_902628965.1_AH-324-F03_genomic.fna/markers.fasta -db /var/lib/cwl/stgea380155-b405-4a3b-a2e0-707bba509fe6/dqc_reference/reference_markers.fasta -out GCA_902628965.1_AH-324-F03_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 08:21:05,345] [INFO] Task succeeded: Blastn
[2023-06-05 08:21:05,349] [INFO] Selected 13 target genomes.
[2023-06-05 08:21:05,350] [INFO] Target genome list was writen to GCA_902628965.1_AH-324-F03_genomic.fna/target_genomes.txt
[2023-06-05 08:21:05,353] [INFO] Task started: fastANI
[2023-06-05 08:21:05,353] [INFO] Running command: fastANI --query /var/lib/cwl/stg996d073b-916a-4c18-8668-ed020be078b8/GCA_902628965.1_AH-324-F03_genomic.fna.gz --refList GCA_902628965.1_AH-324-F03_genomic.fna/target_genomes.txt --output GCA_902628965.1_AH-324-F03_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 08:21:11,136] [INFO] Task succeeded: fastANI
[2023-06-05 08:21:11,136] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea380155-b405-4a3b-a2e0-707bba509fe6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 08:21:11,137] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea380155-b405-4a3b-a2e0-707bba509fe6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 08:21:11,143] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 08:21:11,143] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 08:21:11,143] [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
Candidatus Pelagibacter ubique	strain=HTCC1062	GCA_000012345.1	198252	198252	suspected-type	True	78.4678	191	392	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 08:21:11,146] [INFO] DFAST Taxonomy check result was written to GCA_902628965.1_AH-324-F03_genomic.fna/tc_result.tsv
[2023-06-05 08:21:11,146] [INFO] ===== Taxonomy check completed =====
[2023-06-05 08:21:11,147] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 08:21:11,147] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea380155-b405-4a3b-a2e0-707bba509fe6/dqc_reference/checkm_data
[2023-06-05 08:21:11,149] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 08:21:11,163] [INFO] Task started: CheckM
[2023-06-05 08:21:11,163] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902628965.1_AH-324-F03_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902628965.1_AH-324-F03_genomic.fna/checkm_input GCA_902628965.1_AH-324-F03_genomic.fna/checkm_result
[2023-06-05 08:21:28,649] [INFO] Task succeeded: CheckM
[2023-06-05 08:21:28,650] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.43%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 08:21:28,670] [INFO] ===== Completeness check finished =====
[2023-06-05 08:21:28,671] [INFO] ===== Start GTDB Search =====
[2023-06-05 08:21:28,671] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902628965.1_AH-324-F03_genomic.fna/markers.fasta)
[2023-06-05 08:21:28,671] [INFO] Task started: Blastn
[2023-06-05 08:21:28,672] [INFO] Running command: blastn -query GCA_902628965.1_AH-324-F03_genomic.fna/markers.fasta -db /var/lib/cwl/stgea380155-b405-4a3b-a2e0-707bba509fe6/dqc_reference/reference_markers_gtdb.fasta -out GCA_902628965.1_AH-324-F03_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 08:21:29,597] [INFO] Task succeeded: Blastn
[2023-06-05 08:21:29,603] [INFO] Selected 24 target genomes.
[2023-06-05 08:21:29,603] [INFO] Target genome list was writen to GCA_902628965.1_AH-324-F03_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 08:21:29,615] [INFO] Task started: fastANI
[2023-06-05 08:21:29,616] [INFO] Running command: fastANI --query /var/lib/cwl/stg996d073b-916a-4c18-8668-ed020be078b8/GCA_902628965.1_AH-324-F03_genomic.fna.gz --refList GCA_902628965.1_AH-324-F03_genomic.fna/target_genomes_gtdb.txt --output GCA_902628965.1_AH-324-F03_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 08:21:34,927] [INFO] Task succeeded: fastANI
[2023-06-05 08:21:34,951] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 08:21:34,951] [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
GCA_902628965.1	s__Pelagibacter sp902628965	100.0	389	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902632545.1	s__Pelagibacter sp902632545	89.1743	263	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902592545.1	s__Pelagibacter sp902592545	88.9986	226	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902527415.1	s__Pelagibacter sp902527415	88.84	238	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902558585.1	s__Pelagibacter sp902558585	88.6503	196	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902558835.1	s__Pelagibacter sp902558835	88.5915	256	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902615975.1	s__Pelagibacter sp902615975	88.4676	290	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902635515.1	s__Pelagibacter sp902635515	88.3444	280	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902532645.1	s__Pelagibacter sp902532645	88.3406	187	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902624015.1	s__Pelagibacter sp902624015	88.2745	216	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902559935.1	s__Pelagibacter sp902559935	88.2115	185	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902593235.1	s__Pelagibacter sp902593235	88.0737	224	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902588315.1	s__Pelagibacter sp902588315	88.0255	270	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902571135.1	s__Pelagibacter sp902571135	88.0216	274	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902593405.1	s__Pelagibacter sp902593405	87.8217	261	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902619745.1	s__Pelagibacter sp902619745	87.7795	234	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902618695.1	s__Pelagibacter sp902618695	87.675	286	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	99.78	99.78	0.87	0.87	2	-
GCA_902578325.1	s__Pelagibacter sp902578325	87.573	213	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902616165.1	s__Pelagibacter sp902616165	87.5569	166	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902596375.1	s__Pelagibacter sp902596375	87.4742	246	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902587755.1	s__Pelagibacter sp902587755	87.2168	299	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902600245.1	s__Pelagibacter sp902600245	86.3044	196	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003279765.1	s__Pelagibacter sp003279765	82.0824	179	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_902548405.1	s__Pelagibacter sp902548405	81.3309	202	392	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	95.45	95.45	0.65	0.65	2	-
--------------------------------------------------------------------------------
[2023-06-05 08:21:34,954] [INFO] GTDB search result was written to GCA_902628965.1_AH-324-F03_genomic.fna/result_gtdb.tsv
[2023-06-05 08:21:34,955] [INFO] ===== GTDB Search completed =====
[2023-06-05 08:21:34,960] [INFO] DFAST_QC result json was written to GCA_902628965.1_AH-324-F03_genomic.fna/dqc_result.json
[2023-06-05 08:21:34,960] [INFO] DFAST_QC completed!
[2023-06-05 08:21:34,960] [INFO] Total running time: 0h0m36s