[2023-03-18 05:35:37,310] [INFO] DFAST_QC pipeline started.
[2023-03-18 05:35:37,313] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 05:35:37,313] [INFO] DQC Reference Directory: /var/lib/cwl/stg0324c817-2e09-4287-bd9e-ddb46a7c4c1c/dqc_reference
[2023-03-18 05:35:38,965] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 05:35:38,965] [INFO] Task started: Prodigal
[2023-03-18 05:35:38,965] [INFO] Running command: cat /var/lib/cwl/stgb724ea14-a13b-4f8d-ad6e-015cf953cb6e/OceanDNA-b20545.fa | prodigal -d OceanDNA-b20545/cds.fna -a OceanDNA-b20545/protein.faa -g 11 -q > /dev/null
[2023-03-18 05:35:45,821] [INFO] Task succeeded: Prodigal
[2023-03-18 05:35:45,821] [INFO] Task started: HMMsearch
[2023-03-18 05:35:45,821] [INFO] Running command: hmmsearch --tblout OceanDNA-b20545/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0324c817-2e09-4287-bd9e-ddb46a7c4c1c/dqc_reference/reference_markers.hmm OceanDNA-b20545/protein.faa > /dev/null
[2023-03-18 05:35:46,007] [INFO] Task succeeded: HMMsearch
[2023-03-18 05:35:46,008] [INFO] Found 6/6 markers.
[2023-03-18 05:35:46,044] [INFO] Query marker FASTA was written to OceanDNA-b20545/markers.fasta
[2023-03-18 05:35:46,047] [INFO] Task started: Blastn
[2023-03-18 05:35:46,047] [INFO] Running command: blastn -query OceanDNA-b20545/markers.fasta -db /var/lib/cwl/stg0324c817-2e09-4287-bd9e-ddb46a7c4c1c/dqc_reference/reference_markers.fasta -out OceanDNA-b20545/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:35:46,608] [INFO] Task succeeded: Blastn
[2023-03-18 05:35:46,618] [INFO] Selected 20 target genomes.
[2023-03-18 05:35:46,619] [INFO] Target genome list was writen to OceanDNA-b20545/target_genomes.txt
[2023-03-18 05:35:46,627] [INFO] Task started: fastANI
[2023-03-18 05:35:46,627] [INFO] Running command: fastANI --query /var/lib/cwl/stgb724ea14-a13b-4f8d-ad6e-015cf953cb6e/OceanDNA-b20545.fa --refList OceanDNA-b20545/target_genomes.txt --output OceanDNA-b20545/fastani_result.tsv --threads 1
[2023-03-18 05:35:55,487] [INFO] Task succeeded: fastANI
[2023-03-18 05:35:55,487] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0324c817-2e09-4287-bd9e-ddb46a7c4c1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 05:35:55,487] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0324c817-2e09-4287-bd9e-ddb46a7c4c1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 05:35:55,487] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 05:35:55,488] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 05:35:55,488] [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 05:35:55,488] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20545/tc_result.tsv
[2023-03-18 05:35:55,490] [INFO] ===== Taxonomy check completed =====
[2023-03-18 05:35:55,490] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 05:35:55,490] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0324c817-2e09-4287-bd9e-ddb46a7c4c1c/dqc_reference/checkm_data
[2023-03-18 05:35:55,494] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 05:35:55,498] [INFO] Task started: CheckM
[2023-03-18 05:35:55,498] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20545/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20545/checkm_input OceanDNA-b20545/checkm_result
[2023-03-18 05:36:18,194] [INFO] Task succeeded: CheckM
[2023-03-18 05:36:18,194] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 05:36:18,234] [INFO] ===== Completeness check finished =====
[2023-03-18 05:36:18,234] [INFO] ===== Start GTDB Search =====
[2023-03-18 05:36:18,235] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20545/markers.fasta)
[2023-03-18 05:36:18,236] [INFO] Task started: Blastn
[2023-03-18 05:36:18,236] [INFO] Running command: blastn -query OceanDNA-b20545/markers.fasta -db /var/lib/cwl/stg0324c817-2e09-4287-bd9e-ddb46a7c4c1c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20545/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:36:19,160] [INFO] Task succeeded: Blastn
[2023-03-18 05:36:19,164] [INFO] Selected 14 target genomes.
[2023-03-18 05:36:19,164] [INFO] Target genome list was writen to OceanDNA-b20545/target_genomes_gtdb.txt
[2023-03-18 05:36:19,175] [INFO] Task started: fastANI
[2023-03-18 05:36:19,176] [INFO] Running command: fastANI --query /var/lib/cwl/stgb724ea14-a13b-4f8d-ad6e-015cf953cb6e/OceanDNA-b20545.fa --refList OceanDNA-b20545/target_genomes_gtdb.txt --output OceanDNA-b20545/fastani_result_gtdb.tsv --threads 1
[2023-03-18 05:36:22,885] [INFO] Task succeeded: fastANI
[2023-03-18 05:36:22,889] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 05:36:22,889] [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_002704685.1	s__GCA-002707645 sp002704685	99.1562	436	461	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__GCA-002707645;g__GCA-002707645	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002693365.1	s__GCA-002707645 sp002693365	93.6358	360	461	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__GCA-002707645;g__GCA-002707645	95.0	98.01	98.01	0.73	0.73	2	-
GCA_002705605.1	s__GCA-002707645 sp002705605	80.1473	312	461	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__GCA-002707645;g__GCA-002707645	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002707645.1	s__GCA-002707645 sp002707645	80.095	270	461	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__GCA-002707645;g__GCA-002707645	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002717625.1	s__GCA-2717625 sp002717625	76.3444	85	461	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__GCA-002707645;g__GCA-2717625	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 05:36:22,891] [INFO] GTDB search result was written to OceanDNA-b20545/result_gtdb.tsv
[2023-03-18 05:36:22,892] [INFO] ===== GTDB Search completed =====
[2023-03-18 05:36:22,895] [INFO] DFAST_QC result json was written to OceanDNA-b20545/dqc_result.json
[2023-03-18 05:36:22,895] [INFO] DFAST_QC completed!
[2023-03-18 05:36:22,895] [INFO] Total running time: 0h0m46s