[2023-03-18 22:44:58,039] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:44:58,040] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:44:58,040] [INFO] DQC Reference Directory: /var/lib/cwl/stg15d7243b-4e37-46b9-a07c-f2b3285b4655/dqc_reference
[2023-03-18 22:44:59,138] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:44:59,139] [INFO] Task started: Prodigal
[2023-03-18 22:44:59,139] [INFO] Running command: cat /var/lib/cwl/stg77b355dc-17dc-45bb-ad43-4f01d9533b33/OceanDNA-a1288.fa | prodigal -d OceanDNA-a1288/cds.fna -a OceanDNA-a1288/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:45:01,375] [INFO] Task succeeded: Prodigal
[2023-03-18 22:45:01,376] [INFO] Task started: HMMsearch
[2023-03-18 22:45:01,376] [INFO] Running command: hmmsearch --tblout OceanDNA-a1288/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg15d7243b-4e37-46b9-a07c-f2b3285b4655/dqc_reference/reference_markers.hmm OceanDNA-a1288/protein.faa > /dev/null
[2023-03-18 22:45:01,467] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:45:01,467] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg77b355dc-17dc-45bb-ad43-4f01d9533b33/OceanDNA-a1288.fa]
[2023-03-18 22:45:01,483] [INFO] Query marker FASTA was written to OceanDNA-a1288/markers.fasta
[2023-03-18 22:45:01,485] [INFO] Task started: Blastn
[2023-03-18 22:45:01,485] [INFO] Running command: blastn -query OceanDNA-a1288/markers.fasta -db /var/lib/cwl/stg15d7243b-4e37-46b9-a07c-f2b3285b4655/dqc_reference/reference_markers.fasta -out OceanDNA-a1288/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:45:01,940] [INFO] Task succeeded: Blastn
[2023-03-18 22:45:01,943] [INFO] Selected 0 target genomes.
[2023-03-18 22:45:01,943] [INFO] Target genome list was writen to OceanDNA-a1288/target_genomes.txt
[2023-03-18 22:45:01,943] [ERROR] File is empty. [OceanDNA-a1288/target_genomes.txt]
[2023-03-18 22:45:01,943] [ERROR] Task failed. No target genome found.
[2023-03-18 22:45:01,943] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:45:01,944] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg15d7243b-4e37-46b9-a07c-f2b3285b4655/dqc_reference/checkm_data
[2023-03-18 22:45:01,997] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:45:02,000] [INFO] Task started: CheckM
[2023-03-18 22:45:02,001] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1288/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1288/checkm_input OceanDNA-a1288/checkm_result
[2023-03-18 22:45:15,841] [INFO] Task succeeded: CheckM
[2023-03-18 22:45:15,841] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.79%
Contamintation: 1.39%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 22:45:15,888] [INFO] ===== Completeness check finished =====
[2023-03-18 22:45:15,889] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:45:15,889] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1288/markers.fasta)
[2023-03-18 22:45:15,890] [INFO] Task started: Blastn
[2023-03-18 22:45:15,890] [INFO] Running command: blastn -query OceanDNA-a1288/markers.fasta -db /var/lib/cwl/stg15d7243b-4e37-46b9-a07c-f2b3285b4655/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1288/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:45:16,482] [INFO] Task succeeded: Blastn
[2023-03-18 22:45:16,485] [INFO] Selected 3 target genomes.
[2023-03-18 22:45:16,485] [INFO] Target genome list was writen to OceanDNA-a1288/target_genomes_gtdb.txt
[2023-03-18 22:45:16,490] [INFO] Task started: fastANI
[2023-03-18 22:45:16,490] [INFO] Running command: fastANI --query /var/lib/cwl/stg77b355dc-17dc-45bb-ad43-4f01d9533b33/OceanDNA-a1288.fa --refList OceanDNA-a1288/target_genomes_gtdb.txt --output OceanDNA-a1288/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:45:16,879] [INFO] Task succeeded: fastANI
[2023-03-18 22:45:16,881] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 22:45:16,882] [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_014240455.1	s__JAAZWY01 sp014240455	97.4761	124	138	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__UBA10117;f__ARS21;g__JAAZWY01	95.0	98.17	98.17	0.91	0.91	2	conclusive
GCA_018698915.1	s__JAAZWY01 sp018698915	82.6116	102	138	d__Archaea;p__Nanoarchaeota;c__Nanoarchaeia;o__UBA10117;f__ARS21;g__JAAZWY01	95.0	99.92	99.92	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-03-18 22:45:16,883] [INFO] GTDB search result was written to OceanDNA-a1288/result_gtdb.tsv
[2023-03-18 22:45:16,885] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:45:16,888] [INFO] DFAST_QC result json was written to OceanDNA-a1288/dqc_result.json
[2023-03-18 22:45:16,888] [INFO] DFAST_QC completed!
[2023-03-18 22:45:16,888] [INFO] Total running time: 0h0m19s