[2023-03-18 00:02:09,216] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:02:09,216] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:02:09,217] [INFO] DQC Reference Directory: /var/lib/cwl/stg253baf15-c6df-490c-936a-523bc1fa0ebe/dqc_reference
[2023-03-18 00:02:10,370] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:02:10,370] [INFO] Task started: Prodigal
[2023-03-18 00:02:10,371] [INFO] Running command: cat /var/lib/cwl/stgc10b1be4-d0dd-4889-910d-ebae0d8e65a4/OceanDNA-a4139.fa | prodigal -d OceanDNA-a4139/cds.fna -a OceanDNA-a4139/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:02:16,718] [INFO] Task succeeded: Prodigal
[2023-03-18 00:02:16,719] [INFO] Task started: HMMsearch
[2023-03-18 00:02:16,719] [INFO] Running command: hmmsearch --tblout OceanDNA-a4139/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg253baf15-c6df-490c-936a-523bc1fa0ebe/dqc_reference/reference_markers.hmm OceanDNA-a4139/protein.faa > /dev/null
[2023-03-18 00:02:16,827] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:02:16,827] [WARNING] Found 1/6 markers. [/var/lib/cwl/stgc10b1be4-d0dd-4889-910d-ebae0d8e65a4/OceanDNA-a4139.fa]
[2023-03-18 00:02:16,835] [INFO] Query marker FASTA was written to OceanDNA-a4139/markers.fasta
[2023-03-18 00:02:16,836] [INFO] Task started: Blastn
[2023-03-18 00:02:16,836] [INFO] Running command: blastn -query OceanDNA-a4139/markers.fasta -db /var/lib/cwl/stg253baf15-c6df-490c-936a-523bc1fa0ebe/dqc_reference/reference_markers.fasta -out OceanDNA-a4139/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:02:17,237] [INFO] Task succeeded: Blastn
[2023-03-18 00:02:17,237] [INFO] Selected 0 target genomes.
[2023-03-18 00:02:17,238] [INFO] Target genome list was writen to OceanDNA-a4139/target_genomes.txt
[2023-03-18 00:02:17,238] [ERROR] File is empty. [OceanDNA-a4139/target_genomes.txt]
[2023-03-18 00:02:17,238] [ERROR] Task failed. No target genome found.
[2023-03-18 00:02:17,238] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:02:17,238] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg253baf15-c6df-490c-936a-523bc1fa0ebe/dqc_reference/checkm_data
[2023-03-18 00:02:17,289] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:02:17,292] [INFO] Task started: CheckM
[2023-03-18 00:02:17,292] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4139/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4139/checkm_input OceanDNA-a4139/checkm_result
[2023-03-18 00:02:40,028] [INFO] Task succeeded: CheckM
[2023-03-18 00:02:40,029] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.94%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:02:40,030] [INFO] ===== Completeness check finished =====
[2023-03-18 00:02:40,030] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:02:40,030] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4139/markers.fasta)
[2023-03-18 00:02:40,031] [INFO] Task started: Blastn
[2023-03-18 00:02:40,031] [INFO] Running command: blastn -query OceanDNA-a4139/markers.fasta -db /var/lib/cwl/stg253baf15-c6df-490c-936a-523bc1fa0ebe/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4139/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:02:40,391] [INFO] Task succeeded: Blastn
[2023-03-18 00:02:40,392] [INFO] Selected 5 target genomes.
[2023-03-18 00:02:40,392] [INFO] Target genome list was writen to OceanDNA-a4139/target_genomes_gtdb.txt
[2023-03-18 00:02:40,427] [INFO] Task started: fastANI
[2023-03-18 00:02:40,427] [INFO] Running command: fastANI --query /var/lib/cwl/stgc10b1be4-d0dd-4889-910d-ebae0d8e65a4/OceanDNA-a4139.fa --refList OceanDNA-a4139/target_genomes_gtdb.txt --output OceanDNA-a4139/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:02:41,602] [INFO] Task succeeded: fastANI
[2023-03-18 00:02:41,606] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 00:02:41,606] [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_001628485.1	s__MGIIb-O3 sp001628485	91.6356	229	249	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	98.15	97.12	0.88	0.79	10	-
GCA_902573015.1	s__MGIIb-O3 sp902573015	91.5703	156	249	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902625325.1	s__MGIIb-O3 sp902625325	90.6774	213	249	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902601345.1	s__MGIIb-O3 sp902601345	90.2843	194	249	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001629255.1	s__MGIIb-O3 sp001629255	90.1698	213	249	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	98.42	97.36	0.80	0.70	6	-
--------------------------------------------------------------------------------
[2023-03-18 00:02:41,607] [INFO] GTDB search result was written to OceanDNA-a4139/result_gtdb.tsv
[2023-03-18 00:02:41,607] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:02:41,607] [INFO] DFAST_QC result json was written to OceanDNA-a4139/dqc_result.json
[2023-03-18 00:02:41,607] [INFO] DFAST_QC completed!
[2023-03-18 00:02:41,608] [INFO] Total running time: 0h0m32s