[2023-03-14 13:05:43,387] [INFO] DFAST_QC pipeline started.
[2023-03-14 13:05:43,387] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 13:05:43,387] [INFO] DQC Reference Directory: /var/lib/cwl/stgf537fc6e-8ac5-4a7e-8449-e4f947223d20/dqc_reference
[2023-03-14 13:05:44,564] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 13:05:44,565] [INFO] Task started: Prodigal
[2023-03-14 13:05:44,565] [INFO] Running command: cat /var/lib/cwl/stg4c8fdb1b-d866-4428-919b-fcb89080e05a/OceanDNA-b24430.fa | prodigal -d OceanDNA-b24430/cds.fna -a OceanDNA-b24430/protein.faa -g 11 -q > /dev/null
[2023-03-14 13:05:49,474] [INFO] Task succeeded: Prodigal
[2023-03-14 13:05:49,474] [INFO] Task started: HMMsearch
[2023-03-14 13:05:49,474] [INFO] Running command: hmmsearch --tblout OceanDNA-b24430/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf537fc6e-8ac5-4a7e-8449-e4f947223d20/dqc_reference/reference_markers.hmm OceanDNA-b24430/protein.faa > /dev/null
[2023-03-14 13:05:49,654] [INFO] Task succeeded: HMMsearch
[2023-03-14 13:05:49,655] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg4c8fdb1b-d866-4428-919b-fcb89080e05a/OceanDNA-b24430.fa]
[2023-03-14 13:05:49,662] [INFO] Query marker FASTA was written to OceanDNA-b24430/markers.fasta
[2023-03-14 13:05:49,664] [INFO] Task started: Blastn
[2023-03-14 13:05:49,664] [INFO] Running command: blastn -query OceanDNA-b24430/markers.fasta -db /var/lib/cwl/stgf537fc6e-8ac5-4a7e-8449-e4f947223d20/dqc_reference/reference_markers.fasta -out OceanDNA-b24430/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:05:50,242] [INFO] Task succeeded: Blastn
[2023-03-14 13:05:50,243] [INFO] Selected 18 target genomes.
[2023-03-14 13:05:50,243] [INFO] Target genome list was writen to OceanDNA-b24430/target_genomes.txt
[2023-03-14 13:05:50,256] [INFO] Task started: fastANI
[2023-03-14 13:05:50,256] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c8fdb1b-d866-4428-919b-fcb89080e05a/OceanDNA-b24430.fa --refList OceanDNA-b24430/target_genomes.txt --output OceanDNA-b24430/fastani_result.tsv --threads 1
[2023-03-14 13:05:59,740] [INFO] Task succeeded: fastANI
[2023-03-14 13:05:59,740] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf537fc6e-8ac5-4a7e-8449-e4f947223d20/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 13:05:59,740] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf537fc6e-8ac5-4a7e-8449-e4f947223d20/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 13:05:59,741] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 13:05:59,741] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 13:05:59,741] [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
--------------------------------------------------------------------------------
[2023-03-14 13:05:59,741] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24430/tc_result.tsv
[2023-03-14 13:05:59,741] [INFO] ===== Taxonomy check completed =====
[2023-03-14 13:05:59,741] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 13:05:59,741] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf537fc6e-8ac5-4a7e-8449-e4f947223d20/dqc_reference/checkm_data
[2023-03-14 13:05:59,751] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 13:05:59,754] [INFO] Task started: CheckM
[2023-03-14 13:05:59,754] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24430/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24430/checkm_input OceanDNA-b24430/checkm_result
[2023-03-14 13:06:27,370] [INFO] Task succeeded: CheckM
[2023-03-14 13:06:27,371] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.43%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 13:06:27,372] [INFO] ===== Completeness check finished =====
[2023-03-14 13:06:27,372] [INFO] ===== Start GTDB Search =====
[2023-03-14 13:06:27,372] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24430/markers.fasta)
[2023-03-14 13:06:27,374] [INFO] Task started: Blastn
[2023-03-14 13:06:27,374] [INFO] Running command: blastn -query OceanDNA-b24430/markers.fasta -db /var/lib/cwl/stgf537fc6e-8ac5-4a7e-8449-e4f947223d20/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24430/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:06:28,470] [INFO] Task succeeded: Blastn
[2023-03-14 13:06:28,471] [INFO] Selected 17 target genomes.
[2023-03-14 13:06:28,471] [INFO] Target genome list was writen to OceanDNA-b24430/target_genomes_gtdb.txt
[2023-03-14 13:06:28,492] [INFO] Task started: fastANI
[2023-03-14 13:06:28,492] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c8fdb1b-d866-4428-919b-fcb89080e05a/OceanDNA-b24430.fa --refList OceanDNA-b24430/target_genomes_gtdb.txt --output OceanDNA-b24430/fastani_result_gtdb.tsv --threads 1
[2023-03-14 13:06:31,958] [INFO] Task succeeded: fastANI
[2023-03-14 13:06:31,964] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 13:06:31,964] [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_002937895.1	s__PTKV01 sp002937895	99.8919	267	283	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__PTKV01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902567855.1	s__MarineAlpha5-Bin3 sp902567855	76.6427	61	283	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__MarineAlpha5-Bin3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902577425.1	s__MarineAlpha5-Bin3 sp902577425	76.4813	88	283	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__MarineAlpha5-Bin3	95.0	95.54	95.54	0.86	0.86	2	-
GCA_902586695.1	s__AG-337-I02 sp902586695	76.3559	60	283	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902620425.1	s__AG-337-I02 sp902620425	76.1942	64	283	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	95.06	95.06	0.88	0.88	2	-
GCA_902596065.1	s__MarineAlpha5-Bin3 sp902596065	76.062	53	283	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__MarineAlpha5-Bin3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902582755.1	s__AG-337-I02 sp902582755	76.0091	52	283	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	99.81	99.81	0.85	0.85	2	-
GCA_902521315.1	s__AG-337-I02 sp902521315	75.8629	60	283	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902573325.1	s__AG-337-I02 sp902573325	75.7362	57	283	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 13:06:31,965] [INFO] GTDB search result was written to OceanDNA-b24430/result_gtdb.tsv
[2023-03-14 13:06:31,965] [INFO] ===== GTDB Search completed =====
[2023-03-14 13:06:31,966] [INFO] DFAST_QC result json was written to OceanDNA-b24430/dqc_result.json
[2023-03-14 13:06:31,966] [INFO] DFAST_QC completed!
[2023-03-14 13:06:31,966] [INFO] Total running time: 0h0m49s