[2023-03-17 07:47:46,559] [INFO] DFAST_QC pipeline started.
[2023-03-17 07:47:46,559] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 07:47:46,559] [INFO] DQC Reference Directory: /var/lib/cwl/stgac34538c-5000-4251-b770-c96ed4136756/dqc_reference
[2023-03-17 07:47:47,683] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 07:47:47,683] [INFO] Task started: Prodigal
[2023-03-17 07:47:47,683] [INFO] Running command: cat /var/lib/cwl/stg32cfbe51-43b5-44f7-98cb-89ef467758f3/OceanDNA-b24461.fa | prodigal -d OceanDNA-b24461/cds.fna -a OceanDNA-b24461/protein.faa -g 11 -q > /dev/null
[2023-03-17 07:47:53,878] [INFO] Task succeeded: Prodigal
[2023-03-17 07:47:53,878] [INFO] Task started: HMMsearch
[2023-03-17 07:47:53,878] [INFO] Running command: hmmsearch --tblout OceanDNA-b24461/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgac34538c-5000-4251-b770-c96ed4136756/dqc_reference/reference_markers.hmm OceanDNA-b24461/protein.faa > /dev/null
[2023-03-17 07:47:54,020] [INFO] Task succeeded: HMMsearch
[2023-03-17 07:47:54,020] [INFO] Found 6/6 markers.
[2023-03-17 07:47:54,029] [INFO] Query marker FASTA was written to OceanDNA-b24461/markers.fasta
[2023-03-17 07:47:54,029] [INFO] Task started: Blastn
[2023-03-17 07:47:54,029] [INFO] Running command: blastn -query OceanDNA-b24461/markers.fasta -db /var/lib/cwl/stgac34538c-5000-4251-b770-c96ed4136756/dqc_reference/reference_markers.fasta -out OceanDNA-b24461/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:47:54,529] [INFO] Task succeeded: Blastn
[2023-03-17 07:47:54,530] [INFO] Selected 15 target genomes.
[2023-03-17 07:47:54,530] [INFO] Target genome list was writen to OceanDNA-b24461/target_genomes.txt
[2023-03-17 07:47:54,537] [INFO] Task started: fastANI
[2023-03-17 07:47:54,537] [INFO] Running command: fastANI --query /var/lib/cwl/stg32cfbe51-43b5-44f7-98cb-89ef467758f3/OceanDNA-b24461.fa --refList OceanDNA-b24461/target_genomes.txt --output OceanDNA-b24461/fastani_result.tsv --threads 1
[2023-03-17 07:47:59,694] [INFO] Task succeeded: fastANI
[2023-03-17 07:47:59,695] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgac34538c-5000-4251-b770-c96ed4136756/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 07:47:59,695] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgac34538c-5000-4251-b770-c96ed4136756/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 07:47:59,695] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 07:47:59,695] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 07:47:59,695] [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
--------------------------------------------------------------------------------
[2023-03-17 07:47:59,695] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24461/tc_result.tsv
[2023-03-17 07:47:59,695] [INFO] ===== Taxonomy check completed =====
[2023-03-17 07:47:59,695] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 07:47:59,696] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgac34538c-5000-4251-b770-c96ed4136756/dqc_reference/checkm_data
[2023-03-17 07:47:59,698] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 07:47:59,700] [INFO] Task started: CheckM
[2023-03-17 07:47:59,700] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24461/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24461/checkm_input OceanDNA-b24461/checkm_result
[2023-03-17 07:48:20,692] [INFO] Task succeeded: CheckM
[2023-03-17 07:48:20,692] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 07:48:20,694] [INFO] ===== Completeness check finished =====
[2023-03-17 07:48:20,694] [INFO] ===== Start GTDB Search =====
[2023-03-17 07:48:20,694] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24461/markers.fasta)
[2023-03-17 07:48:20,694] [INFO] Task started: Blastn
[2023-03-17 07:48:20,694] [INFO] Running command: blastn -query OceanDNA-b24461/markers.fasta -db /var/lib/cwl/stgac34538c-5000-4251-b770-c96ed4136756/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24461/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:48:21,412] [INFO] Task succeeded: Blastn
[2023-03-17 07:48:21,413] [INFO] Selected 25 target genomes.
[2023-03-17 07:48:21,413] [INFO] Target genome list was writen to OceanDNA-b24461/target_genomes_gtdb.txt
[2023-03-17 07:48:21,716] [INFO] Task started: fastANI
[2023-03-17 07:48:21,716] [INFO] Running command: fastANI --query /var/lib/cwl/stg32cfbe51-43b5-44f7-98cb-89ef467758f3/OceanDNA-b24461.fa --refList OceanDNA-b24461/target_genomes_gtdb.txt --output OceanDNA-b24461/fastani_result_gtdb.tsv --threads 1
[2023-03-17 07:48:26,850] [INFO] Task succeeded: fastANI
[2023-03-17 07:48:26,855] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 07:48:26,856] [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_002705265.1	s__HIMB59 sp002705265	78.0236	133	346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000299115.1	s__HIMB59 sp000299115	76.5531	61	346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902521155.1	s__HIMB59 sp902521155	76.3745	59	346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	99.50	99.50	0.70	0.70	2	-
GCA_902599045.1	s__HIMB59 sp902615815	76.3645	65	346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	96.41	95.18	0.86	0.81	23	-
GCA_902527045.1	s__HIMB59 sp902527045	76.2314	71	346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902527545.1	s__HIMB59 sp902527545	76.0356	69	346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	99.61	99.43	0.88	0.87	4	-
GCA_902591315.1	s__HIMB59 sp902591315	75.9588	51	346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	95.30	95.30	0.78	0.78	2	-
GCA_004321805.1	s__HIMB59 sp004321805	75.8147	54	346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 07:48:26,856] [INFO] GTDB search result was written to OceanDNA-b24461/result_gtdb.tsv
[2023-03-17 07:48:26,856] [INFO] ===== GTDB Search completed =====
[2023-03-17 07:48:26,857] [INFO] DFAST_QC result json was written to OceanDNA-b24461/dqc_result.json
[2023-03-17 07:48:26,857] [INFO] DFAST_QC completed!
[2023-03-17 07:48:26,857] [INFO] Total running time: 0h0m40s