[2023-03-15 07:03:38,936] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:03:38,938] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:03:38,938] [INFO] DQC Reference Directory: /var/lib/cwl/stg2d08616a-63b2-4f89-88b0-1732c827beef/dqc_reference
[2023-03-15 07:03:40,047] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:03:40,047] [INFO] Task started: Prodigal
[2023-03-15 07:03:40,047] [INFO] Running command: cat /var/lib/cwl/stg6feeb00e-cb7b-42b2-99d0-ff41a7c10c9c/OceanDNA-a3771.fa | prodigal -d OceanDNA-a3771/cds.fna -a OceanDNA-a3771/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:03:44,161] [INFO] Task succeeded: Prodigal
[2023-03-15 07:03:44,161] [INFO] Task started: HMMsearch
[2023-03-15 07:03:44,161] [INFO] Running command: hmmsearch --tblout OceanDNA-a3771/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2d08616a-63b2-4f89-88b0-1732c827beef/dqc_reference/reference_markers.hmm OceanDNA-a3771/protein.faa > /dev/null
[2023-03-15 07:03:44,283] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:03:44,284] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg6feeb00e-cb7b-42b2-99d0-ff41a7c10c9c/OceanDNA-a3771.fa]
[2023-03-15 07:03:44,312] [INFO] Query marker FASTA was written to OceanDNA-a3771/markers.fasta
[2023-03-15 07:03:44,312] [INFO] Task started: Blastn
[2023-03-15 07:03:44,312] [INFO] Running command: blastn -query OceanDNA-a3771/markers.fasta -db /var/lib/cwl/stg2d08616a-63b2-4f89-88b0-1732c827beef/dqc_reference/reference_markers.fasta -out OceanDNA-a3771/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:03:44,746] [INFO] Task succeeded: Blastn
[2023-03-15 07:03:44,752] [INFO] Selected 0 target genomes.
[2023-03-15 07:03:44,752] [INFO] Target genome list was writen to OceanDNA-a3771/target_genomes.txt
[2023-03-15 07:03:44,752] [ERROR] File is empty. [OceanDNA-a3771/target_genomes.txt]
[2023-03-15 07:03:44,752] [ERROR] Task failed. No target genome found.
[2023-03-15 07:03:44,752] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:03:44,753] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2d08616a-63b2-4f89-88b0-1732c827beef/dqc_reference/checkm_data
[2023-03-15 07:03:44,806] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:03:44,811] [INFO] Task started: CheckM
[2023-03-15 07:03:44,811] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a3771/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a3771/checkm_input OceanDNA-a3771/checkm_result
[2023-03-15 07:04:02,225] [INFO] Task succeeded: CheckM
[2023-03-15 07:04:02,225] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 07:04:02,282] [INFO] ===== Completeness check finished =====
[2023-03-15 07:04:02,282] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:04:02,282] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a3771/markers.fasta)
[2023-03-15 07:04:02,282] [INFO] Task started: Blastn
[2023-03-15 07:04:02,283] [INFO] Running command: blastn -query OceanDNA-a3771/markers.fasta -db /var/lib/cwl/stg2d08616a-63b2-4f89-88b0-1732c827beef/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a3771/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:04:03,193] [INFO] Task succeeded: Blastn
[2023-03-15 07:04:03,201] [INFO] Selected 5 target genomes.
[2023-03-15 07:04:03,201] [INFO] Target genome list was writen to OceanDNA-a3771/target_genomes_gtdb.txt
[2023-03-15 07:04:03,232] [INFO] Task started: fastANI
[2023-03-15 07:04:03,232] [INFO] Running command: fastANI --query /var/lib/cwl/stg6feeb00e-cb7b-42b2-99d0-ff41a7c10c9c/OceanDNA-a3771.fa --refList OceanDNA-a3771/target_genomes_gtdb.txt --output OceanDNA-a3771/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:04:04,288] [INFO] Task succeeded: fastANI
[2023-03-15 07:04:04,291] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 07:04:04,291] [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_902511005.1	s__MGIIb-O2 sp902511005	79.3171	134	252	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O2	95.0	98.72	98.72	0.78	0.78	2	-
GCA_002497245.1	s__MGIIb-O2 sp002497245	77.8846	123	252	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O2	95.0	97.50	97.50	0.90	0.90	2	-
GCA_002498985.1	s__MGIIb-O2 sp002498985	77.6458	92	252	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O2	95.0	97.30	95.20	0.78	0.62	4	-
--------------------------------------------------------------------------------
[2023-03-15 07:04:04,293] [INFO] GTDB search result was written to OceanDNA-a3771/result_gtdb.tsv
[2023-03-15 07:04:04,299] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:04:04,303] [INFO] DFAST_QC result json was written to OceanDNA-a3771/dqc_result.json
[2023-03-15 07:04:04,303] [INFO] DFAST_QC completed!
[2023-03-15 07:04:04,303] [INFO] Total running time: 0h0m25s