[2023-03-18 22:02:41,369] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:02:41,369] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:02:41,370] [INFO] DQC Reference Directory: /var/lib/cwl/stg985c825a-0a39-4b66-820f-f67eece4b81f/dqc_reference
[2023-03-18 22:02:42,497] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:02:42,498] [INFO] Task started: Prodigal
[2023-03-18 22:02:42,498] [INFO] Running command: cat /var/lib/cwl/stg2f0e96ba-5fd5-40e6-a87a-9d8ac5dc5b99/OceanDNA-a4447.fa | prodigal -d OceanDNA-a4447/cds.fna -a OceanDNA-a4447/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:02:48,526] [INFO] Task succeeded: Prodigal
[2023-03-18 22:02:48,526] [INFO] Task started: HMMsearch
[2023-03-18 22:02:48,526] [INFO] Running command: hmmsearch --tblout OceanDNA-a4447/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg985c825a-0a39-4b66-820f-f67eece4b81f/dqc_reference/reference_markers.hmm OceanDNA-a4447/protein.faa > /dev/null
[2023-03-18 22:02:48,679] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:02:48,679] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg2f0e96ba-5fd5-40e6-a87a-9d8ac5dc5b99/OceanDNA-a4447.fa]
[2023-03-18 22:02:48,688] [INFO] Query marker FASTA was written to OceanDNA-a4447/markers.fasta
[2023-03-18 22:02:48,689] [INFO] Task started: Blastn
[2023-03-18 22:02:48,689] [INFO] Running command: blastn -query OceanDNA-a4447/markers.fasta -db /var/lib/cwl/stg985c825a-0a39-4b66-820f-f67eece4b81f/dqc_reference/reference_markers.fasta -out OceanDNA-a4447/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:02:49,302] [INFO] Task succeeded: Blastn
[2023-03-18 22:02:49,303] [INFO] Selected 0 target genomes.
[2023-03-18 22:02:49,303] [INFO] Target genome list was writen to OceanDNA-a4447/target_genomes.txt
[2023-03-18 22:02:49,303] [ERROR] File is empty. [OceanDNA-a4447/target_genomes.txt]
[2023-03-18 22:02:49,304] [ERROR] Task failed. No target genome found.
[2023-03-18 22:02:49,304] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:02:49,304] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg985c825a-0a39-4b66-820f-f67eece4b81f/dqc_reference/checkm_data
[2023-03-18 22:02:49,350] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:02:49,353] [INFO] Task started: CheckM
[2023-03-18 22:02:49,353] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4447/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4447/checkm_input OceanDNA-a4447/checkm_result
[2023-03-18 22:03:12,218] [INFO] Task succeeded: CheckM
[2023-03-18 22:03:12,219] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.21%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 22:03:12,221] [INFO] ===== Completeness check finished =====
[2023-03-18 22:03:12,221] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:03:12,221] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4447/markers.fasta)
[2023-03-18 22:03:12,223] [INFO] Task started: Blastn
[2023-03-18 22:03:12,223] [INFO] Running command: blastn -query OceanDNA-a4447/markers.fasta -db /var/lib/cwl/stg985c825a-0a39-4b66-820f-f67eece4b81f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4447/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:03:12,901] [INFO] Task succeeded: Blastn
[2023-03-18 22:03:12,902] [INFO] Selected 1 target genomes.
[2023-03-18 22:03:12,902] [INFO] Target genome list was writen to OceanDNA-a4447/target_genomes_gtdb.txt
[2023-03-18 22:03:12,905] [INFO] Task started: fastANI
[2023-03-18 22:03:12,905] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f0e96ba-5fd5-40e6-a87a-9d8ac5dc5b99/OceanDNA-a4447.fa --refList OceanDNA-a4447/target_genomes_gtdb.txt --output OceanDNA-a4447/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:03:13,216] [INFO] Task succeeded: fastANI
[2023-03-18 22:03:13,218] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 22:03:13,219] [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_002504435.1	s__MGIIb-O5 sp002504435	86.499	285	341	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O5	95.0	99.62	99.62	0.76	0.76	2	-
--------------------------------------------------------------------------------
[2023-03-18 22:03:13,219] [INFO] GTDB search result was written to OceanDNA-a4447/result_gtdb.tsv
[2023-03-18 22:03:13,219] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:03:13,220] [INFO] DFAST_QC result json was written to OceanDNA-a4447/dqc_result.json
[2023-03-18 22:03:13,220] [INFO] DFAST_QC completed!
[2023-03-18 22:03:13,220] [INFO] Total running time: 0h0m32s