[2023-03-16 09:50:49,898] [INFO] DFAST_QC pipeline started.
[2023-03-16 09:50:49,905] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 09:50:49,906] [INFO] DQC Reference Directory: /var/lib/cwl/stgd01d1938-0526-48c3-a3dc-296523a0d4a9/dqc_reference
[2023-03-16 09:50:51,042] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 09:50:51,042] [INFO] Task started: Prodigal
[2023-03-16 09:50:51,042] [INFO] Running command: cat /var/lib/cwl/stgd8ee6d49-d7f9-43a0-865c-ab10d275cbde/OceanDNA-b19419.fa | prodigal -d OceanDNA-b19419/cds.fna -a OceanDNA-b19419/protein.faa -g 11 -q > /dev/null
[2023-03-16 09:50:56,374] [INFO] Task succeeded: Prodigal
[2023-03-16 09:50:56,375] [INFO] Task started: HMMsearch
[2023-03-16 09:50:56,375] [INFO] Running command: hmmsearch --tblout OceanDNA-b19419/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd01d1938-0526-48c3-a3dc-296523a0d4a9/dqc_reference/reference_markers.hmm OceanDNA-b19419/protein.faa > /dev/null
[2023-03-16 09:50:56,522] [INFO] Task succeeded: HMMsearch
[2023-03-16 09:50:56,522] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgd8ee6d49-d7f9-43a0-865c-ab10d275cbde/OceanDNA-b19419.fa]
[2023-03-16 09:50:56,577] [INFO] Query marker FASTA was written to OceanDNA-b19419/markers.fasta
[2023-03-16 09:50:56,578] [INFO] Task started: Blastn
[2023-03-16 09:50:56,578] [INFO] Running command: blastn -query OceanDNA-b19419/markers.fasta -db /var/lib/cwl/stgd01d1938-0526-48c3-a3dc-296523a0d4a9/dqc_reference/reference_markers.fasta -out OceanDNA-b19419/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:50:57,016] [INFO] Task succeeded: Blastn
[2023-03-16 09:50:57,040] [INFO] Selected 11 target genomes.
[2023-03-16 09:50:57,040] [INFO] Target genome list was writen to OceanDNA-b19419/target_genomes.txt
[2023-03-16 09:50:57,051] [INFO] Task started: fastANI
[2023-03-16 09:50:57,051] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8ee6d49-d7f9-43a0-865c-ab10d275cbde/OceanDNA-b19419.fa --refList OceanDNA-b19419/target_genomes.txt --output OceanDNA-b19419/fastani_result.tsv --threads 1
[2023-03-16 09:51:02,668] [INFO] Task succeeded: fastANI
[2023-03-16 09:51:02,668] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd01d1938-0526-48c3-a3dc-296523a0d4a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 09:51:02,668] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd01d1938-0526-48c3-a3dc-296523a0d4a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 09:51:02,668] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 09:51:02,668] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 09:51:02,669] [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
--------------------------------------------------------------------------------
[2023-03-16 09:51:02,676] [INFO] DFAST Taxonomy check result was written to OceanDNA-b19419/tc_result.tsv
[2023-03-16 09:51:02,692] [INFO] ===== Taxonomy check completed =====
[2023-03-16 09:51:02,692] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 09:51:02,692] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd01d1938-0526-48c3-a3dc-296523a0d4a9/dqc_reference/checkm_data
[2023-03-16 09:51:02,695] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 09:51:02,701] [INFO] Task started: CheckM
[2023-03-16 09:51:02,701] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b19419/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b19419/checkm_input OceanDNA-b19419/checkm_result
[2023-03-16 09:51:22,124] [INFO] Task succeeded: CheckM
[2023-03-16 09:51:22,124] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.86%
Contamintation: 2.60%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-16 09:51:22,206] [INFO] ===== Completeness check finished =====
[2023-03-16 09:51:22,207] [INFO] ===== Start GTDB Search =====
[2023-03-16 09:51:22,207] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b19419/markers.fasta)
[2023-03-16 09:51:22,208] [INFO] Task started: Blastn
[2023-03-16 09:51:22,208] [INFO] Running command: blastn -query OceanDNA-b19419/markers.fasta -db /var/lib/cwl/stgd01d1938-0526-48c3-a3dc-296523a0d4a9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b19419/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:51:22,639] [INFO] Task succeeded: Blastn
[2023-03-16 09:51:22,665] [INFO] Selected 14 target genomes.
[2023-03-16 09:51:22,665] [INFO] Target genome list was writen to OceanDNA-b19419/target_genomes_gtdb.txt
[2023-03-16 09:51:22,732] [INFO] Task started: fastANI
[2023-03-16 09:51:22,732] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8ee6d49-d7f9-43a0-865c-ab10d275cbde/OceanDNA-b19419.fa --refList OceanDNA-b19419/target_genomes_gtdb.txt --output OceanDNA-b19419/fastani_result_gtdb.tsv --threads 1
[2023-03-16 09:51:27,442] [INFO] Task succeeded: fastANI
[2023-03-16 09:51:27,444] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 09:51:27,444] [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_002725545.1	s__TMED108 sp002725545	98.3367	250	326	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TMED108	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002712245.1	s__TMED108 sp002712245	93.1837	179	326	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__TCS55;g__TMED108	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 09:51:27,447] [INFO] GTDB search result was written to OceanDNA-b19419/result_gtdb.tsv
[2023-03-16 09:51:27,449] [INFO] ===== GTDB Search completed =====
[2023-03-16 09:51:27,453] [INFO] DFAST_QC result json was written to OceanDNA-b19419/dqc_result.json
[2023-03-16 09:51:27,453] [INFO] DFAST_QC completed!
[2023-03-16 09:51:27,453] [INFO] Total running time: 0h0m38s