[2023-06-05 18:51:53,054] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:51:53,060] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:51:53,060] [INFO] DQC Reference Directory: /var/lib/cwl/stg8e56a38a-a559-48eb-9387-ce5b23d81deb/dqc_reference
[2023-06-05 18:51:54,606] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:51:54,607] [INFO] Task started: Prodigal
[2023-06-05 18:51:54,607] [INFO] Running command: gunzip -c /var/lib/cwl/stg9c11b6b7-e7a2-4bcb-b593-54d454509ef2/GCA_902524015.1_AG-895-I23_genomic.fna.gz | prodigal -d GCA_902524015.1_AG-895-I23_genomic.fna/cds.fna -a GCA_902524015.1_AG-895-I23_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:51:56,246] [INFO] Task succeeded: Prodigal
[2023-06-05 18:51:56,246] [INFO] Task started: HMMsearch
[2023-06-05 18:51:56,246] [INFO] Running command: hmmsearch --tblout GCA_902524015.1_AG-895-I23_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8e56a38a-a559-48eb-9387-ce5b23d81deb/dqc_reference/reference_markers.hmm GCA_902524015.1_AG-895-I23_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:51:56,431] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:51:56,433] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg9c11b6b7-e7a2-4bcb-b593-54d454509ef2/GCA_902524015.1_AG-895-I23_genomic.fna.gz]
[2023-06-05 18:51:56,448] [INFO] Query marker FASTA was written to GCA_902524015.1_AG-895-I23_genomic.fna/markers.fasta
[2023-06-05 18:51:56,448] [INFO] Task started: Blastn
[2023-06-05 18:51:56,448] [INFO] Running command: blastn -query GCA_902524015.1_AG-895-I23_genomic.fna/markers.fasta -db /var/lib/cwl/stg8e56a38a-a559-48eb-9387-ce5b23d81deb/dqc_reference/reference_markers.fasta -out GCA_902524015.1_AG-895-I23_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:51:56,966] [INFO] Task succeeded: Blastn
[2023-06-05 18:51:57,002] [INFO] Selected 9 target genomes.
[2023-06-05 18:51:57,003] [INFO] Target genome list was writen to GCA_902524015.1_AG-895-I23_genomic.fna/target_genomes.txt
[2023-06-05 18:51:57,012] [INFO] Task started: fastANI
[2023-06-05 18:51:57,012] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c11b6b7-e7a2-4bcb-b593-54d454509ef2/GCA_902524015.1_AG-895-I23_genomic.fna.gz --refList GCA_902524015.1_AG-895-I23_genomic.fna/target_genomes.txt --output GCA_902524015.1_AG-895-I23_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:52:00,040] [INFO] Task succeeded: fastANI
[2023-06-05 18:52:00,041] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8e56a38a-a559-48eb-9387-ce5b23d81deb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:52:00,041] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8e56a38a-a559-48eb-9387-ce5b23d81deb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:52:00,045] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:52:00,045] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 18:52:00,045] [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	78.3882	80	166	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 18:52:00,047] [INFO] DFAST Taxonomy check result was written to GCA_902524015.1_AG-895-I23_genomic.fna/tc_result.tsv
[2023-06-05 18:52:00,048] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:52:00,048] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:52:00,048] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8e56a38a-a559-48eb-9387-ce5b23d81deb/dqc_reference/checkm_data
[2023-06-05 18:52:00,049] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:52:00,059] [INFO] Task started: CheckM
[2023-06-05 18:52:00,060] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902524015.1_AG-895-I23_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902524015.1_AG-895-I23_genomic.fna/checkm_input GCA_902524015.1_AG-895-I23_genomic.fna/checkm_result
[2023-06-05 18:52:13,687] [INFO] Task succeeded: CheckM
[2023-06-05 18:52:13,689] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:52:13,707] [INFO] ===== Completeness check finished =====
[2023-06-05 18:52:13,707] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:52:13,708] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902524015.1_AG-895-I23_genomic.fna/markers.fasta)
[2023-06-05 18:52:13,708] [INFO] Task started: Blastn
[2023-06-05 18:52:13,708] [INFO] Running command: blastn -query GCA_902524015.1_AG-895-I23_genomic.fna/markers.fasta -db /var/lib/cwl/stg8e56a38a-a559-48eb-9387-ce5b23d81deb/dqc_reference/reference_markers_gtdb.fasta -out GCA_902524015.1_AG-895-I23_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:52:14,885] [INFO] Task succeeded: Blastn
[2023-06-05 18:52:14,891] [INFO] Selected 18 target genomes.
[2023-06-05 18:52:14,892] [INFO] Target genome list was writen to GCA_902524015.1_AG-895-I23_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:52:14,905] [INFO] Task started: fastANI
[2023-06-05 18:52:14,906] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c11b6b7-e7a2-4bcb-b593-54d454509ef2/GCA_902524015.1_AG-895-I23_genomic.fna.gz --refList GCA_902524015.1_AG-895-I23_genomic.fna/target_genomes_gtdb.txt --output GCA_902524015.1_AG-895-I23_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:52:18,234] [INFO] Task succeeded: fastANI
[2023-06-05 18:52:18,250] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 18:52:18,251] [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_902568855.1	s__Pelagibacter sp902568855	92.9783	69	166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902578265.1	s__Pelagibacter sp902578265	92.8018	134	166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	99.64	99.64	0.82	0.82	2	-
GCA_902629535.1	s__Pelagibacter sp902629535	92.2051	99	166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902576375.1	s__Pelagibacter sp902576375	91.9908	136	166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902565385.1	s__Pelagibacter sp902565385	91.7014	106	166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902617625.1	s__Pelagibacter sp902617625	91.3232	133	166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902596925.1	s__Pelagibacter sp902596925	91.0626	135	166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	96.28	96.07	0.86	0.84	3	-
GCA_902520335.1	s__Pelagibacter sp902520335	90.7377	136	166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	99.90	99.90	0.86	0.86	2	-
GCA_902597725.1	s__Pelagibacter sp902597725	90.6598	102	166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902600635.1	s__Pelagibacter sp902600635	90.4271	86	166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902592265.1	s__Pelagibacter sp902592265	89.7374	124	166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902625035.1	s__Pelagibacter sp902625035	88.9476	118	166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902520355.1	s__Pelagibacter sp902520355	87.8298	79	166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902633585.1	s__Pelagibacter sp902633585	86.501	104	166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902543375.1	s__Pelagibacter sp902543375	86.3673	108	166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	99.27	99.27	0.91	0.91	2	-
GCA_003282055.1	s__Pelagibacter sp003282055	84.3164	71	166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902540275.1	s__Pelagibacter sp902540275	81.6745	90	166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003278065.1	s__Pelagibacter sp003278065	80.5769	100	166	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-06-05 18:52:18,256] [INFO] GTDB search result was written to GCA_902524015.1_AG-895-I23_genomic.fna/result_gtdb.tsv
[2023-06-05 18:52:18,260] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:52:18,266] [INFO] DFAST_QC result json was written to GCA_902524015.1_AG-895-I23_genomic.fna/dqc_result.json
[2023-06-05 18:52:18,266] [INFO] DFAST_QC completed!
[2023-06-05 18:52:18,267] [INFO] Total running time: 0h0m25s