[2023-03-14 14:50:59,121] [INFO] DFAST_QC pipeline started.
[2023-03-14 14:50:59,121] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 14:50:59,121] [INFO] DQC Reference Directory: /var/lib/cwl/stg63f410b7-10c3-47c4-aaf7-5e212523f2a6/dqc_reference
[2023-03-14 14:51:00,238] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 14:51:00,238] [INFO] Task started: Prodigal
[2023-03-14 14:51:00,238] [INFO] Running command: cat /var/lib/cwl/stg12ba4c50-3068-4ef8-bab4-fbf8e621def9/OceanDNA-a1795.fa | prodigal -d OceanDNA-a1795/cds.fna -a OceanDNA-a1795/protein.faa -g 11 -q > /dev/null
[2023-03-14 14:51:02,315] [INFO] Task succeeded: Prodigal
[2023-03-14 14:51:02,315] [INFO] Task started: HMMsearch
[2023-03-14 14:51:02,315] [INFO] Running command: hmmsearch --tblout OceanDNA-a1795/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg63f410b7-10c3-47c4-aaf7-5e212523f2a6/dqc_reference/reference_markers.hmm OceanDNA-a1795/protein.faa > /dev/null
[2023-03-14 14:51:02,464] [INFO] Task succeeded: HMMsearch
[2023-03-14 14:51:02,465] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg12ba4c50-3068-4ef8-bab4-fbf8e621def9/OceanDNA-a1795.fa]
[2023-03-14 14:51:02,471] [INFO] Query marker FASTA was written to OceanDNA-a1795/markers.fasta
[2023-03-14 14:51:02,473] [INFO] Task started: Blastn
[2023-03-14 14:51:02,473] [INFO] Running command: blastn -query OceanDNA-a1795/markers.fasta -db /var/lib/cwl/stg63f410b7-10c3-47c4-aaf7-5e212523f2a6/dqc_reference/reference_markers.fasta -out OceanDNA-a1795/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:51:03,017] [INFO] Task succeeded: Blastn
[2023-03-14 14:51:03,019] [INFO] Selected 1 target genomes.
[2023-03-14 14:51:03,019] [INFO] Target genome list was writen to OceanDNA-a1795/target_genomes.txt
[2023-03-14 14:51:03,020] [INFO] Task started: fastANI
[2023-03-14 14:51:03,020] [INFO] Running command: fastANI --query /var/lib/cwl/stg12ba4c50-3068-4ef8-bab4-fbf8e621def9/OceanDNA-a1795.fa --refList OceanDNA-a1795/target_genomes.txt --output OceanDNA-a1795/fastani_result.tsv --threads 1
[2023-03-14 14:51:03,429] [INFO] Task succeeded: fastANI
[2023-03-14 14:51:03,429] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg63f410b7-10c3-47c4-aaf7-5e212523f2a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 14:51:03,430] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg63f410b7-10c3-47c4-aaf7-5e212523f2a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 14:51:03,430] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 14:51:03,430] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 14:51:03,430] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
--------------------------------------------------------------------------------
[2023-03-14 14:51:03,431] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1795/tc_result.tsv
[2023-03-14 14:51:03,431] [INFO] ===== Taxonomy check completed =====
[2023-03-14 14:51:03,431] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 14:51:03,432] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg63f410b7-10c3-47c4-aaf7-5e212523f2a6/dqc_reference/checkm_data
[2023-03-14 14:51:03,485] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 14:51:03,554] [INFO] Task started: CheckM
[2023-03-14 14:51:03,554] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1795/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1795/checkm_input OceanDNA-a1795/checkm_result
[2023-03-14 14:51:20,366] [INFO] Task succeeded: CheckM
[2023-03-14 14:51:20,366] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.45%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 14:51:20,369] [INFO] ===== Completeness check finished =====
[2023-03-14 14:51:20,369] [INFO] ===== Start GTDB Search =====
[2023-03-14 14:51:20,369] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1795/markers.fasta)
[2023-03-14 14:51:20,375] [INFO] Task started: Blastn
[2023-03-14 14:51:20,375] [INFO] Running command: blastn -query OceanDNA-a1795/markers.fasta -db /var/lib/cwl/stg63f410b7-10c3-47c4-aaf7-5e212523f2a6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1795/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:51:22,252] [INFO] Task succeeded: Blastn
[2023-03-14 14:51:22,253] [INFO] Selected 5 target genomes.
[2023-03-14 14:51:22,253] [INFO] Target genome list was writen to OceanDNA-a1795/target_genomes_gtdb.txt
[2023-03-14 14:51:22,260] [INFO] Task started: fastANI
[2023-03-14 14:51:22,260] [INFO] Running command: fastANI --query /var/lib/cwl/stg12ba4c50-3068-4ef8-bab4-fbf8e621def9/OceanDNA-a1795.fa --refList OceanDNA-a1795/target_genomes_gtdb.txt --output OceanDNA-a1795/fastani_result_gtdb.tsv --threads 1
[2023-03-14 14:51:24,626] [INFO] Task succeeded: fastANI
[2023-03-14 14:51:24,628] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 14:51:24,628] [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_001875425.1	s__UBA102 sp001875425	81.0104	96	123	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__UBA102	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002509225.1	s__UBA102 sp002509225	80.0327	91	123	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__UBA102	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 14:51:24,629] [INFO] GTDB search result was written to OceanDNA-a1795/result_gtdb.tsv
[2023-03-14 14:51:24,629] [INFO] ===== GTDB Search completed =====
[2023-03-14 14:51:24,630] [INFO] DFAST_QC result json was written to OceanDNA-a1795/dqc_result.json
[2023-03-14 14:51:24,631] [INFO] DFAST_QC completed!
[2023-03-14 14:51:24,631] [INFO] Total running time: 0h0m26s