[2023-03-16 16:26:08,363] [INFO] DFAST_QC pipeline started.
[2023-03-16 16:26:08,363] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 16:26:08,363] [INFO] DQC Reference Directory: /var/lib/cwl/stgfd1923a5-d633-4bb1-af9b-4a0068ff0047/dqc_reference
[2023-03-16 16:26:10,861] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 16:26:10,862] [INFO] Task started: Prodigal
[2023-03-16 16:26:10,862] [INFO] Running command: cat /var/lib/cwl/stg5d31aa7f-21cf-42f6-a8e1-f6ea825a24d1/OceanDNA-a3356.fa | prodigal -d OceanDNA-a3356/cds.fna -a OceanDNA-a3356/protein.faa -g 11 -q > /dev/null
[2023-03-16 16:26:16,644] [INFO] Task succeeded: Prodigal
[2023-03-16 16:26:16,644] [INFO] Task started: HMMsearch
[2023-03-16 16:26:16,644] [INFO] Running command: hmmsearch --tblout OceanDNA-a3356/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfd1923a5-d633-4bb1-af9b-4a0068ff0047/dqc_reference/reference_markers.hmm OceanDNA-a3356/protein.faa > /dev/null
[2023-03-16 16:26:16,912] [INFO] Task succeeded: HMMsearch
[2023-03-16 16:26:16,913] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg5d31aa7f-21cf-42f6-a8e1-f6ea825a24d1/OceanDNA-a3356.fa]
[2023-03-16 16:26:16,926] [INFO] Query marker FASTA was written to OceanDNA-a3356/markers.fasta
[2023-03-16 16:26:16,927] [INFO] Task started: Blastn
[2023-03-16 16:26:16,927] [INFO] Running command: blastn -query OceanDNA-a3356/markers.fasta -db /var/lib/cwl/stgfd1923a5-d633-4bb1-af9b-4a0068ff0047/dqc_reference/reference_markers.fasta -out OceanDNA-a3356/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:26:17,972] [INFO] Task succeeded: Blastn
[2023-03-16 16:26:17,973] [INFO] Selected 5 target genomes.
[2023-03-16 16:26:17,973] [INFO] Target genome list was writen to OceanDNA-a3356/target_genomes.txt
[2023-03-16 16:26:17,978] [INFO] Task started: fastANI
[2023-03-16 16:26:17,978] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d31aa7f-21cf-42f6-a8e1-f6ea825a24d1/OceanDNA-a3356.fa --refList OceanDNA-a3356/target_genomes.txt --output OceanDNA-a3356/fastani_result.tsv --threads 1
[2023-03-16 16:26:21,322] [INFO] Task succeeded: fastANI
[2023-03-16 16:26:21,322] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfd1923a5-d633-4bb1-af9b-4a0068ff0047/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 16:26:21,323] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfd1923a5-d633-4bb1-af9b-4a0068ff0047/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 16:26:21,323] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 16:26:21,323] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 16:26:21,323] [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 16:26:21,323] [INFO] DFAST Taxonomy check result was written to OceanDNA-a3356/tc_result.tsv
[2023-03-16 16:26:21,323] [INFO] ===== Taxonomy check completed =====
[2023-03-16 16:26:21,323] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 16:26:21,323] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfd1923a5-d633-4bb1-af9b-4a0068ff0047/dqc_reference/checkm_data
[2023-03-16 16:26:21,377] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 16:26:21,381] [INFO] Task started: CheckM
[2023-03-16 16:26:21,381] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a3356/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a3356/checkm_input OceanDNA-a3356/checkm_result
[2023-03-16 16:26:50,936] [INFO] Task succeeded: CheckM
[2023-03-16 16:26:50,937] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.40%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 16:26:50,938] [INFO] ===== Completeness check finished =====
[2023-03-16 16:26:50,939] [INFO] ===== Start GTDB Search =====
[2023-03-16 16:26:50,939] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a3356/markers.fasta)
[2023-03-16 16:26:50,939] [INFO] Task started: Blastn
[2023-03-16 16:26:50,939] [INFO] Running command: blastn -query OceanDNA-a3356/markers.fasta -db /var/lib/cwl/stgfd1923a5-d633-4bb1-af9b-4a0068ff0047/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a3356/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:26:51,714] [INFO] Task succeeded: Blastn
[2023-03-16 16:26:51,715] [INFO] Selected 8 target genomes.
[2023-03-16 16:26:51,715] [INFO] Target genome list was writen to OceanDNA-a3356/target_genomes_gtdb.txt
[2023-03-16 16:26:51,890] [INFO] Task started: fastANI
[2023-03-16 16:26:51,890] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d31aa7f-21cf-42f6-a8e1-f6ea825a24d1/OceanDNA-a3356.fa --refList OceanDNA-a3356/target_genomes_gtdb.txt --output OceanDNA-a3356/fastani_result_gtdb.tsv --threads 1
[2023-03-16 16:26:54,098] [INFO] Task succeeded: fastANI
[2023-03-16 16:26:54,103] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 16:26:54,103] [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_002697105.1	s__MGIIb-N2 sp002697105	89.7594	217	310	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-N2	95.0	96.01	96.01	0.68	0.68	2	-
GCA_002702985.1	s__MGIIb-N2 sp002702985	88.5294	242	310	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-N2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002708015.1	s__MGIIb-N2 sp002708015	87.9613	251	310	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-N2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002502625.1	s__MGIIb-N2 sp002502625	87.2222	281	310	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-N2	95.0	99.71	99.70	0.87	0.83	3	-
GCA_002503045.1	s__MGIIb-N2 sp002503045	79.516	164	310	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-N2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002503665.1	s__MGIIb-N2 sp002503665	78.1364	88	310	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-N2	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 16:26:54,103] [INFO] GTDB search result was written to OceanDNA-a3356/result_gtdb.tsv
[2023-03-16 16:26:54,103] [INFO] ===== GTDB Search completed =====
[2023-03-16 16:26:54,104] [INFO] DFAST_QC result json was written to OceanDNA-a3356/dqc_result.json
[2023-03-16 16:26:54,104] [INFO] DFAST_QC completed!
[2023-03-16 16:26:54,104] [INFO] Total running time: 0h0m46s