[2023-03-16 06:03:00,928] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:03:00,928] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:03:00,928] [INFO] DQC Reference Directory: /var/lib/cwl/stg48da1321-744d-448f-902d-c4dccc68bd19/dqc_reference
[2023-03-16 06:03:02,044] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:03:02,044] [INFO] Task started: Prodigal
[2023-03-16 06:03:02,044] [INFO] Running command: cat /var/lib/cwl/stg430f34fe-d7be-4de6-b09f-05bd3dce85a5/OceanDNA-a113.fa | prodigal -d OceanDNA-a113/cds.fna -a OceanDNA-a113/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:03:04,374] [INFO] Task succeeded: Prodigal
[2023-03-16 06:03:04,374] [INFO] Task started: HMMsearch
[2023-03-16 06:03:04,374] [INFO] Running command: hmmsearch --tblout OceanDNA-a113/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg48da1321-744d-448f-902d-c4dccc68bd19/dqc_reference/reference_markers.hmm OceanDNA-a113/protein.faa > /dev/null
[2023-03-16 06:03:04,491] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:03:04,491] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg430f34fe-d7be-4de6-b09f-05bd3dce85a5/OceanDNA-a113.fa]
[2023-03-16 06:03:04,512] [INFO] Query marker FASTA was written to OceanDNA-a113/markers.fasta
[2023-03-16 06:03:04,514] [INFO] Task started: Blastn
[2023-03-16 06:03:04,514] [INFO] Running command: blastn -query OceanDNA-a113/markers.fasta -db /var/lib/cwl/stg48da1321-744d-448f-902d-c4dccc68bd19/dqc_reference/reference_markers.fasta -out OceanDNA-a113/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:03:04,966] [INFO] Task succeeded: Blastn
[2023-03-16 06:03:04,974] [INFO] Selected 0 target genomes.
[2023-03-16 06:03:04,974] [INFO] Target genome list was writen to OceanDNA-a113/target_genomes.txt
[2023-03-16 06:03:04,974] [ERROR] File is empty. [OceanDNA-a113/target_genomes.txt]
[2023-03-16 06:03:04,974] [ERROR] Task failed. No target genome found.
[2023-03-16 06:03:04,974] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:03:04,975] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg48da1321-744d-448f-902d-c4dccc68bd19/dqc_reference/checkm_data
[2023-03-16 06:03:04,978] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:03:04,981] [INFO] Task started: CheckM
[2023-03-16 06:03:04,981] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a113/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a113/checkm_input OceanDNA-a113/checkm_result
[2023-03-16 06:03:18,413] [INFO] Task succeeded: CheckM
[2023-03-16 06:03:18,413] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.66%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 06:03:18,441] [INFO] ===== Completeness check finished =====
[2023-03-16 06:03:18,441] [INFO] ===== Start GTDB Search =====
[2023-03-16 06:03:18,441] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a113/markers.fasta)
[2023-03-16 06:03:18,443] [INFO] Task started: Blastn
[2023-03-16 06:03:18,443] [INFO] Running command: blastn -query OceanDNA-a113/markers.fasta -db /var/lib/cwl/stg48da1321-744d-448f-902d-c4dccc68bd19/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a113/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:03:18,856] [INFO] Task succeeded: Blastn
[2023-03-16 06:03:18,865] [INFO] Selected 5 target genomes.
[2023-03-16 06:03:18,865] [INFO] Target genome list was writen to OceanDNA-a113/target_genomes_gtdb.txt
[2023-03-16 06:03:18,872] [INFO] Task started: fastANI
[2023-03-16 06:03:18,872] [INFO] Running command: fastANI --query /var/lib/cwl/stg430f34fe-d7be-4de6-b09f-05bd3dce85a5/OceanDNA-a113.fa --refList OceanDNA-a113/target_genomes_gtdb.txt --output OceanDNA-a113/fastani_result_gtdb.tsv --threads 1
[2023-03-16 06:03:19,740] [INFO] Task succeeded: fastANI
[2023-03-16 06:03:19,744] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 06:03:19,744] [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_018263495.1	s__Nitrosopelagicus sp018263495	98.4035	117	132	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000402075.1	s__Nitrosopelagicus sp000402075	94.1875	127	132	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	95.01	95.01	0.87	0.87	2	-
GCA_013390745.1	s__Nitrosopelagicus sp013390745	94.1251	117	132	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013390375.1	s__Nitrosopelagicus sp000484935	88.9514	124	132	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	97.75	96.12	0.83	0.80	4	-
GCA_013390785.1	s__Nitrosopelagicus sp013390785	87.7069	104	132	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopelagicus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 06:03:19,748] [INFO] GTDB search result was written to OceanDNA-a113/result_gtdb.tsv
[2023-03-16 06:03:19,753] [INFO] ===== GTDB Search completed =====
[2023-03-16 06:03:19,758] [INFO] DFAST_QC result json was written to OceanDNA-a113/dqc_result.json
[2023-03-16 06:03:19,758] [INFO] DFAST_QC completed!
[2023-03-16 06:03:19,758] [INFO] Total running time: 0h0m19s