[2023-06-05 10:12:24,645] [INFO] DFAST_QC pipeline started.
[2023-06-05 10:12:24,648] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 10:12:24,649] [INFO] DQC Reference Directory: /var/lib/cwl/stg9a040b69-0de5-4249-817d-e094220bdf8b/dqc_reference
[2023-06-05 10:12:26,678] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 10:12:26,679] [INFO] Task started: Prodigal
[2023-06-05 10:12:26,680] [INFO] Running command: gunzip -c /var/lib/cwl/stg27d73be3-2ef8-488d-a17e-9d31332f2b1f/GCA_010022305.1_ASM1002230v1_genomic.fna.gz | prodigal -d GCA_010022305.1_ASM1002230v1_genomic.fna/cds.fna -a GCA_010022305.1_ASM1002230v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 10:12:28,955] [INFO] Task succeeded: Prodigal
[2023-06-05 10:12:28,955] [INFO] Task started: HMMsearch
[2023-06-05 10:12:28,956] [INFO] Running command: hmmsearch --tblout GCA_010022305.1_ASM1002230v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9a040b69-0de5-4249-817d-e094220bdf8b/dqc_reference/reference_markers.hmm GCA_010022305.1_ASM1002230v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 10:12:29,154] [INFO] Task succeeded: HMMsearch
[2023-06-05 10:12:29,156] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg27d73be3-2ef8-488d-a17e-9d31332f2b1f/GCA_010022305.1_ASM1002230v1_genomic.fna.gz]
[2023-06-05 10:12:29,171] [INFO] Query marker FASTA was written to GCA_010022305.1_ASM1002230v1_genomic.fna/markers.fasta
[2023-06-05 10:12:29,171] [INFO] Task started: Blastn
[2023-06-05 10:12:29,172] [INFO] Running command: blastn -query GCA_010022305.1_ASM1002230v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a040b69-0de5-4249-817d-e094220bdf8b/dqc_reference/reference_markers.fasta -out GCA_010022305.1_ASM1002230v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 10:12:30,724] [INFO] Task succeeded: Blastn
[2023-06-05 10:12:30,728] [INFO] Selected 10 target genomes.
[2023-06-05 10:12:30,729] [INFO] Target genome list was writen to GCA_010022305.1_ASM1002230v1_genomic.fna/target_genomes.txt
[2023-06-05 10:12:30,731] [INFO] Task started: fastANI
[2023-06-05 10:12:30,731] [INFO] Running command: fastANI --query /var/lib/cwl/stg27d73be3-2ef8-488d-a17e-9d31332f2b1f/GCA_010022305.1_ASM1002230v1_genomic.fna.gz --refList GCA_010022305.1_ASM1002230v1_genomic.fna/target_genomes.txt --output GCA_010022305.1_ASM1002230v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 10:12:34,397] [INFO] Task succeeded: fastANI
[2023-06-05 10:12:34,398] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9a040b69-0de5-4249-817d-e094220bdf8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 10:12:34,398] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9a040b69-0de5-4249-817d-e094220bdf8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 10:12:34,404] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 10:12:34,404] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 10:12:34,404] [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	79.0712	88	155	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 10:12:34,407] [INFO] DFAST Taxonomy check result was written to GCA_010022305.1_ASM1002230v1_genomic.fna/tc_result.tsv
[2023-06-05 10:12:34,407] [INFO] ===== Taxonomy check completed =====
[2023-06-05 10:12:34,408] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 10:12:34,408] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9a040b69-0de5-4249-817d-e094220bdf8b/dqc_reference/checkm_data
[2023-06-05 10:12:34,410] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 10:12:34,426] [INFO] Task started: CheckM
[2023-06-05 10:12:34,427] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_010022305.1_ASM1002230v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_010022305.1_ASM1002230v1_genomic.fna/checkm_input GCA_010022305.1_ASM1002230v1_genomic.fna/checkm_result
[2023-06-05 10:12:50,255] [INFO] Task succeeded: CheckM
[2023-06-05 10:12:50,257] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.41%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 10:12:50,275] [INFO] ===== Completeness check finished =====
[2023-06-05 10:12:50,276] [INFO] ===== Start GTDB Search =====
[2023-06-05 10:12:50,276] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_010022305.1_ASM1002230v1_genomic.fna/markers.fasta)
[2023-06-05 10:12:50,276] [INFO] Task started: Blastn
[2023-06-05 10:12:50,277] [INFO] Running command: blastn -query GCA_010022305.1_ASM1002230v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a040b69-0de5-4249-817d-e094220bdf8b/dqc_reference/reference_markers_gtdb.fasta -out GCA_010022305.1_ASM1002230v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 10:12:51,080] [INFO] Task succeeded: Blastn
[2023-06-05 10:12:51,084] [INFO] Selected 14 target genomes.
[2023-06-05 10:12:51,085] [INFO] Target genome list was writen to GCA_010022305.1_ASM1002230v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 10:12:51,087] [INFO] Task started: fastANI
[2023-06-05 10:12:51,087] [INFO] Running command: fastANI --query /var/lib/cwl/stg27d73be3-2ef8-488d-a17e-9d31332f2b1f/GCA_010022305.1_ASM1002230v1_genomic.fna.gz --refList GCA_010022305.1_ASM1002230v1_genomic.fna/target_genomes_gtdb.txt --output GCA_010022305.1_ASM1002230v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 10:12:54,075] [INFO] Task succeeded: fastANI
[2023-06-05 10:12:54,182] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 10:12:54,183] [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_001438335.1	s__Pelagibacter sp001438335	88.6835	120	155	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	99.22	99.14	0.76	0.74	4	-
GCA_008638165.1	s__Pelagibacter sp008638165	80.0118	88	155	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	98.93	98.78	0.83	0.76	5	-
GCF_900177485.1	s__Pelagibacter sp900177485	79.7459	100	155	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017880265.1	s__Pelagibacter sp017880265	79.5776	84	155	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	97.65	97.65	0.82	0.82	2	-
GCA_902596045.1	s__Pelagibacter sp902596045	79.351	87	155	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	95.47	95.47	0.83	0.83	2	-
GCF_000155895.1	s__Pelagibacter sp000155895	79.2215	102	155	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	96.42	95.11	0.93	0.90	6	-
GCA_014653375.1	s__Pelagibacter sp014653375	78.8638	72	155	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	95.97	95.97	0.83	0.83	2	-
GCA_003282975.1	s__Pelagibacter sp003282975	78.6349	87	155	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003279685.1	s__Pelagibacter sp003279685	78.4402	105	155	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_902540595.1	s__Pelagibacter sp902540595	78.344	78	155	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	95.43	95.31	0.77	0.75	3	-
GCA_003209915.1	s__Pelagibacter sp003209915	78.2769	78	155	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	96.70	95.04	0.84	0.76	80	-
GCA_902539165.1	s__Pelagibacter sp902539165	78.0667	79	155	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	98.84	98.84	0.84	0.84	2	-
GCA_902515625.1	s__Pelagibacter sp902515625	77.6136	52	155	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 10:12:54,185] [INFO] GTDB search result was written to GCA_010022305.1_ASM1002230v1_genomic.fna/result_gtdb.tsv
[2023-06-05 10:12:54,186] [INFO] ===== GTDB Search completed =====
[2023-06-05 10:12:54,190] [INFO] DFAST_QC result json was written to GCA_010022305.1_ASM1002230v1_genomic.fna/dqc_result.json
[2023-06-05 10:12:54,190] [INFO] DFAST_QC completed!
[2023-06-05 10:12:54,191] [INFO] Total running time: 0h0m30s