[2023-03-16 06:58:28,754] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:58:28,754] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:58:28,755] [INFO] DQC Reference Directory: /var/lib/cwl/stgef625eee-562b-4513-82ce-ac03ede6cccc/dqc_reference
[2023-03-16 06:58:29,965] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:58:29,965] [INFO] Task started: Prodigal
[2023-03-16 06:58:29,965] [INFO] Running command: cat /var/lib/cwl/stg6c6aa4ff-f0d0-45fd-9d38-9999f3431e22/OceanDNA-b46834.fa | prodigal -d OceanDNA-b46834/cds.fna -a OceanDNA-b46834/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:58:58,431] [INFO] Task succeeded: Prodigal
[2023-03-16 06:58:58,431] [INFO] Task started: HMMsearch
[2023-03-16 06:58:58,431] [INFO] Running command: hmmsearch --tblout OceanDNA-b46834/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgef625eee-562b-4513-82ce-ac03ede6cccc/dqc_reference/reference_markers.hmm OceanDNA-b46834/protein.faa > /dev/null
[2023-03-16 06:58:58,638] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:58:58,639] [INFO] Found 6/6 markers.
[2023-03-16 06:58:58,662] [INFO] Query marker FASTA was written to OceanDNA-b46834/markers.fasta
[2023-03-16 06:58:58,663] [INFO] Task started: Blastn
[2023-03-16 06:58:58,663] [INFO] Running command: blastn -query OceanDNA-b46834/markers.fasta -db /var/lib/cwl/stgef625eee-562b-4513-82ce-ac03ede6cccc/dqc_reference/reference_markers.fasta -out OceanDNA-b46834/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:58:59,217] [INFO] Task succeeded: Blastn
[2023-03-16 06:58:59,218] [INFO] Selected 8 target genomes.
[2023-03-16 06:58:59,218] [INFO] Target genome list was writen to OceanDNA-b46834/target_genomes.txt
[2023-03-16 06:58:59,223] [INFO] Task started: fastANI
[2023-03-16 06:58:59,223] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c6aa4ff-f0d0-45fd-9d38-9999f3431e22/OceanDNA-b46834.fa --refList OceanDNA-b46834/target_genomes.txt --output OceanDNA-b46834/fastani_result.tsv --threads 1
[2023-03-16 06:59:04,346] [INFO] Task succeeded: fastANI
[2023-03-16 06:59:04,347] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgef625eee-562b-4513-82ce-ac03ede6cccc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 06:59:04,347] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgef625eee-562b-4513-82ce-ac03ede6cccc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 06:59:04,347] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 06:59:04,347] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 06:59:04,347] [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 06:59:04,348] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46834/tc_result.tsv
[2023-03-16 06:59:04,348] [INFO] ===== Taxonomy check completed =====
[2023-03-16 06:59:04,348] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:59:04,348] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgef625eee-562b-4513-82ce-ac03ede6cccc/dqc_reference/checkm_data
[2023-03-16 06:59:04,351] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:59:04,403] [INFO] Task started: CheckM
[2023-03-16 06:59:04,403] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46834/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46834/checkm_input OceanDNA-b46834/checkm_result
[2023-03-16 07:00:16,314] [INFO] Task succeeded: CheckM
[2023-03-16 07:00:16,315] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 07:00:16,318] [INFO] ===== Completeness check finished =====
[2023-03-16 07:00:16,318] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:00:16,318] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46834/markers.fasta)
[2023-03-16 07:00:16,319] [INFO] Task started: Blastn
[2023-03-16 07:00:16,319] [INFO] Running command: blastn -query OceanDNA-b46834/markers.fasta -db /var/lib/cwl/stgef625eee-562b-4513-82ce-ac03ede6cccc/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46834/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:00:17,243] [INFO] Task succeeded: Blastn
[2023-03-16 07:00:17,244] [INFO] Selected 12 target genomes.
[2023-03-16 07:00:17,244] [INFO] Target genome list was writen to OceanDNA-b46834/target_genomes_gtdb.txt
[2023-03-16 07:00:17,258] [INFO] Task started: fastANI
[2023-03-16 07:00:17,258] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c6aa4ff-f0d0-45fd-9d38-9999f3431e22/OceanDNA-b46834.fa --refList OceanDNA-b46834/target_genomes_gtdb.txt --output OceanDNA-b46834/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:00:24,030] [INFO] Task succeeded: fastANI
[2023-03-16 07:00:24,035] [INFO] Found 6 fastANI hits (2 hits with ANI > circumscription radius)
[2023-03-16 07:00:24,035] [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_905181965.1	s__SW10 sp905181965	97.8705	720	1178	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__SW10	95.0	97.78	97.70	0.75	0.63	5	inconclusive
GCA_000383735.1	s__SW10 sp000383735	97.0491	528	1178	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__SW10	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_002323895.1	s__SW10 sp002323895	92.4035	916	1178	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__SW10	95.0	99.17	98.66	0.86	0.81	3	-
GCA_002420315.1	s__SW10 sp002420315	87.0191	872	1178	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__SW10	95.0	97.54	96.31	0.84	0.80	11	-
GCA_002729295.1	s__SW10 sp002729295	78.2541	95	1178	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__SW10	95.0	99.31	99.31	0.79	0.79	2	-
GCA_002172625.1	s__SW10 sp002172625	77.755	96	1178	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__SW10	95.0	98.72	98.72	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-03-16 07:00:24,035] [INFO] GTDB search result was written to OceanDNA-b46834/result_gtdb.tsv
[2023-03-16 07:00:24,035] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:00:24,036] [INFO] DFAST_QC result json was written to OceanDNA-b46834/dqc_result.json
[2023-03-16 07:00:24,036] [INFO] DFAST_QC completed!
[2023-03-16 07:00:24,036] [INFO] Total running time: 0h1m55s