[2023-03-18 03:09:33,542] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:09:33,542] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:09:33,542] [INFO] DQC Reference Directory: /var/lib/cwl/stgecae550d-0d79-4ae3-a2d5-351272a07a82/dqc_reference
[2023-03-18 03:09:34,689] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:09:34,689] [INFO] Task started: Prodigal
[2023-03-18 03:09:34,689] [INFO] Running command: cat /var/lib/cwl/stg227ac800-660e-4558-a1d1-9d14b774791c/OceanDNA-b25454.fa | prodigal -d OceanDNA-b25454/cds.fna -a OceanDNA-b25454/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:09:38,447] [INFO] Task succeeded: Prodigal
[2023-03-18 03:09:38,448] [INFO] Task started: HMMsearch
[2023-03-18 03:09:38,448] [INFO] Running command: hmmsearch --tblout OceanDNA-b25454/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgecae550d-0d79-4ae3-a2d5-351272a07a82/dqc_reference/reference_markers.hmm OceanDNA-b25454/protein.faa > /dev/null
[2023-03-18 03:09:38,648] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:09:38,649] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg227ac800-660e-4558-a1d1-9d14b774791c/OceanDNA-b25454.fa]
[2023-03-18 03:09:38,654] [INFO] Query marker FASTA was written to OceanDNA-b25454/markers.fasta
[2023-03-18 03:09:38,656] [INFO] Task started: Blastn
[2023-03-18 03:09:38,656] [INFO] Running command: blastn -query OceanDNA-b25454/markers.fasta -db /var/lib/cwl/stgecae550d-0d79-4ae3-a2d5-351272a07a82/dqc_reference/reference_markers.fasta -out OceanDNA-b25454/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:09:39,226] [INFO] Task succeeded: Blastn
[2023-03-18 03:09:39,226] [INFO] Selected 16 target genomes.
[2023-03-18 03:09:39,227] [INFO] Target genome list was writen to OceanDNA-b25454/target_genomes.txt
[2023-03-18 03:09:39,237] [INFO] Task started: fastANI
[2023-03-18 03:09:39,237] [INFO] Running command: fastANI --query /var/lib/cwl/stg227ac800-660e-4558-a1d1-9d14b774791c/OceanDNA-b25454.fa --refList OceanDNA-b25454/target_genomes.txt --output OceanDNA-b25454/fastani_result.tsv --threads 1
[2023-03-18 03:09:44,509] [INFO] Task succeeded: fastANI
[2023-03-18 03:09:44,510] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgecae550d-0d79-4ae3-a2d5-351272a07a82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:09:44,510] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgecae550d-0d79-4ae3-a2d5-351272a07a82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:09:44,510] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:09:44,510] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 03:09:44,510] [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
--------------------------------------------------------------------------------
[2023-03-18 03:09:44,510] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25454/tc_result.tsv
[2023-03-18 03:09:44,510] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:09:44,510] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:09:44,511] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgecae550d-0d79-4ae3-a2d5-351272a07a82/dqc_reference/checkm_data
[2023-03-18 03:09:44,513] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:09:44,515] [INFO] Task started: CheckM
[2023-03-18 03:09:44,515] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25454/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25454/checkm_input OceanDNA-b25454/checkm_result
[2023-03-18 03:10:02,634] [INFO] Task succeeded: CheckM
[2023-03-18 03:10:02,634] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 51.35%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 03:10:02,635] [INFO] ===== Completeness check finished =====
[2023-03-18 03:10:02,635] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:10:02,636] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25454/markers.fasta)
[2023-03-18 03:10:02,637] [INFO] Task started: Blastn
[2023-03-18 03:10:02,637] [INFO] Running command: blastn -query OceanDNA-b25454/markers.fasta -db /var/lib/cwl/stgecae550d-0d79-4ae3-a2d5-351272a07a82/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25454/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:10:03,661] [INFO] Task succeeded: Blastn
[2023-03-18 03:10:03,662] [INFO] Selected 20 target genomes.
[2023-03-18 03:10:03,662] [INFO] Target genome list was writen to OceanDNA-b25454/target_genomes_gtdb.txt
[2023-03-18 03:10:03,834] [INFO] Task started: fastANI
[2023-03-18 03:10:03,834] [INFO] Running command: fastANI --query /var/lib/cwl/stg227ac800-660e-4558-a1d1-9d14b774791c/OceanDNA-b25454.fa --refList OceanDNA-b25454/target_genomes_gtdb.txt --output OceanDNA-b25454/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:10:07,170] [INFO] Task succeeded: fastANI
[2023-03-18 03:10:07,178] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 03:10:07,178] [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_004213215.1	s__AG-414-E02 sp004213215	99.3854	157	208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902607585.1	s__AG-414-E02 sp902607585	79.9516	74	208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902588335.1	s__AG-414-E02 sp902588335	79.8893	83	208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902607525.1	s__AG-414-E02 sp902607525	79.8197	76	208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902561465.1	s__AG-414-E02 sp902561465	79.7143	83	208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902607625.1	s__AG-414-E02 sp902607625	79.6771	104	208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905612415.1	s__AG-414-E02 sp905612415	79.6754	65	208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905612235.1	s__AG-414-E02 sp905612235	79.4716	80	208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902607735.1	s__AG-414-E02 sp902607735	79.3845	93	208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902608065.1	s__AG-414-E02 sp902608065	79.2169	77	208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902606665.1	s__AG-414-E02 sp902606665	79.0444	78	208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016764285.1	s__AG-414-E02 sp016764285	78.538	91	208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AG-414-E02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003211695.1	s__AAA240-E13 sp003211695	77.347	66	208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__AAA240-E13	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-18 03:10:07,178] [INFO] GTDB search result was written to OceanDNA-b25454/result_gtdb.tsv
[2023-03-18 03:10:07,178] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:10:07,179] [INFO] DFAST_QC result json was written to OceanDNA-b25454/dqc_result.json
[2023-03-18 03:10:07,179] [INFO] DFAST_QC completed!
[2023-03-18 03:10:07,179] [INFO] Total running time: 0h0m34s