[2023-03-19 23:03:45,042] [INFO] DFAST_QC pipeline started.
[2023-03-19 23:03:45,042] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 23:03:45,042] [INFO] DQC Reference Directory: /var/lib/cwl/stgad4b3fd4-3591-444c-b9ce-226f2911fae1/dqc_reference
[2023-03-19 23:03:46,891] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 23:03:46,891] [INFO] Task started: Prodigal
[2023-03-19 23:03:46,891] [INFO] Running command: cat /var/lib/cwl/stg008604a7-f9dc-42d1-b718-e5a44a9b7073/OceanDNA-b10706.fa | prodigal -d OceanDNA-b10706/cds.fna -a OceanDNA-b10706/protein.faa -g 11 -q > /dev/null
[2023-03-19 23:03:58,115] [INFO] Task succeeded: Prodigal
[2023-03-19 23:03:58,115] [INFO] Task started: HMMsearch
[2023-03-19 23:03:58,115] [INFO] Running command: hmmsearch --tblout OceanDNA-b10706/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgad4b3fd4-3591-444c-b9ce-226f2911fae1/dqc_reference/reference_markers.hmm OceanDNA-b10706/protein.faa > /dev/null
[2023-03-19 23:03:58,299] [INFO] Task succeeded: HMMsearch
[2023-03-19 23:03:58,300] [INFO] Found 6/6 markers.
[2023-03-19 23:03:58,312] [INFO] Query marker FASTA was written to OceanDNA-b10706/markers.fasta
[2023-03-19 23:03:58,312] [INFO] Task started: Blastn
[2023-03-19 23:03:58,312] [INFO] Running command: blastn -query OceanDNA-b10706/markers.fasta -db /var/lib/cwl/stgad4b3fd4-3591-444c-b9ce-226f2911fae1/dqc_reference/reference_markers.fasta -out OceanDNA-b10706/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 23:03:58,855] [INFO] Task succeeded: Blastn
[2023-03-19 23:03:58,855] [INFO] Selected 37 target genomes.
[2023-03-19 23:03:58,856] [INFO] Target genome list was writen to OceanDNA-b10706/target_genomes.txt
[2023-03-19 23:03:58,897] [INFO] Task started: fastANI
[2023-03-19 23:03:58,897] [INFO] Running command: fastANI --query /var/lib/cwl/stg008604a7-f9dc-42d1-b718-e5a44a9b7073/OceanDNA-b10706.fa --refList OceanDNA-b10706/target_genomes.txt --output OceanDNA-b10706/fastani_result.tsv --threads 1
[2023-03-19 23:04:18,418] [INFO] Task succeeded: fastANI
[2023-03-19 23:04:18,418] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgad4b3fd4-3591-444c-b9ce-226f2911fae1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 23:04:18,419] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgad4b3fd4-3591-444c-b9ce-226f2911fae1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 23:04:18,419] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 23:04:18,419] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 23:04:18,419] [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
--------------------------------------------------------------------------------
[2023-03-19 23:04:18,419] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10706/tc_result.tsv
[2023-03-19 23:04:18,419] [INFO] ===== Taxonomy check completed =====
[2023-03-19 23:04:18,419] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 23:04:18,419] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgad4b3fd4-3591-444c-b9ce-226f2911fae1/dqc_reference/checkm_data
[2023-03-19 23:04:18,422] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 23:04:18,426] [INFO] Task started: CheckM
[2023-03-19 23:04:18,426] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10706/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10706/checkm_input OceanDNA-b10706/checkm_result
[2023-03-19 23:04:50,861] [INFO] Task succeeded: CheckM
[2023-03-19 23:04:50,862] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.99%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 23:04:50,864] [INFO] ===== Completeness check finished =====
[2023-03-19 23:04:50,864] [INFO] ===== Start GTDB Search =====
[2023-03-19 23:04:50,864] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10706/markers.fasta)
[2023-03-19 23:04:50,864] [INFO] Task started: Blastn
[2023-03-19 23:04:50,864] [INFO] Running command: blastn -query OceanDNA-b10706/markers.fasta -db /var/lib/cwl/stgad4b3fd4-3591-444c-b9ce-226f2911fae1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10706/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 23:04:51,608] [INFO] Task succeeded: Blastn
[2023-03-19 23:04:51,609] [INFO] Selected 25 target genomes.
[2023-03-19 23:04:51,609] [INFO] Target genome list was writen to OceanDNA-b10706/target_genomes_gtdb.txt
[2023-03-19 23:04:51,793] [INFO] Task started: fastANI
[2023-03-19 23:04:51,793] [INFO] Running command: fastANI --query /var/lib/cwl/stg008604a7-f9dc-42d1-b718-e5a44a9b7073/OceanDNA-b10706.fa --refList OceanDNA-b10706/target_genomes_gtdb.txt --output OceanDNA-b10706/fastani_result_gtdb.tsv --threads 1
[2023-03-19 23:05:02,447] [INFO] Task succeeded: fastANI
[2023-03-19 23:05:02,454] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 23:05:02,454] [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_002725015.1	s__UBA3537 sp002725015	99.3489	380	495	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3537	95.0	96.56	95.66	0.77	0.72	3	conclusive
GCA_002690085.1	s__UBA3537 sp002690085	78.3077	178	495	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3537	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002709185.1	s__UBA3537 sp002709185	78.247	154	495	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3537	95.0	98.67	98.67	0.76	0.76	2	-
GCA_002684355.1	s__UBA3537 sp002684355	78.1627	234	495	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3537	95.0	96.40	96.15	0.80	0.77	3	-
GCA_002698705.1	s__UBA3537 sp002698705	77.9366	147	495	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA3537	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001735715.1	s__GCA001735715 sp001735715	77.018	107	495	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA001735715	95.0	98.19	98.19	0.84	0.84	2	-
GCF_001735745.1	s__Hel1-33-131 sp001735745	76.1637	76	495	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479095.1	s__Hel1-33-131 sp905479095	76.1489	62	495	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608725.1	s__Hel1-33-131 sp018608725	76.0924	80	495	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608625.1	s__Hel1-33-131 sp018608625	75.8335	57	495	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	98.93	97.98	0.88	0.82	3	-
GCA_905181825.1	s__Hel1-33-131 sp905181825	75.5995	56	495	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Hel1-33-131	95.0	99.01	99.01	0.77	0.77	2	-
--------------------------------------------------------------------------------
[2023-03-19 23:05:02,454] [INFO] GTDB search result was written to OceanDNA-b10706/result_gtdb.tsv
[2023-03-19 23:05:02,455] [INFO] ===== GTDB Search completed =====
[2023-03-19 23:05:02,456] [INFO] DFAST_QC result json was written to OceanDNA-b10706/dqc_result.json
[2023-03-19 23:05:02,456] [INFO] DFAST_QC completed!
[2023-03-19 23:05:02,456] [INFO] Total running time: 0h1m17s