[2023-03-18 01:43:46,131] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:43:46,133] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:43:46,133] [INFO] DQC Reference Directory: /var/lib/cwl/stg2923a629-87bb-47a9-9b91-cc6b4cd29399/dqc_reference
[2023-03-18 01:43:47,268] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:43:47,268] [INFO] Task started: Prodigal
[2023-03-18 01:43:47,268] [INFO] Running command: cat /var/lib/cwl/stg6c5b6633-cc83-42ac-aa87-6b6c91bfdf0d/OceanDNA-b40185.fa | prodigal -d OceanDNA-b40185/cds.fna -a OceanDNA-b40185/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:44:02,111] [INFO] Task succeeded: Prodigal
[2023-03-18 01:44:02,112] [INFO] Task started: HMMsearch
[2023-03-18 01:44:02,112] [INFO] Running command: hmmsearch --tblout OceanDNA-b40185/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2923a629-87bb-47a9-9b91-cc6b4cd29399/dqc_reference/reference_markers.hmm OceanDNA-b40185/protein.faa > /dev/null
[2023-03-18 01:44:02,292] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:44:02,293] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6c5b6633-cc83-42ac-aa87-6b6c91bfdf0d/OceanDNA-b40185.fa]
[2023-03-18 01:44:02,316] [INFO] Query marker FASTA was written to OceanDNA-b40185/markers.fasta
[2023-03-18 01:44:02,317] [INFO] Task started: Blastn
[2023-03-18 01:44:02,318] [INFO] Running command: blastn -query OceanDNA-b40185/markers.fasta -db /var/lib/cwl/stg2923a629-87bb-47a9-9b91-cc6b4cd29399/dqc_reference/reference_markers.fasta -out OceanDNA-b40185/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:44:02,922] [INFO] Task succeeded: Blastn
[2023-03-18 01:44:02,926] [INFO] Selected 28 target genomes.
[2023-03-18 01:44:02,926] [INFO] Target genome list was writen to OceanDNA-b40185/target_genomes.txt
[2023-03-18 01:44:02,944] [INFO] Task started: fastANI
[2023-03-18 01:44:02,944] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c5b6633-cc83-42ac-aa87-6b6c91bfdf0d/OceanDNA-b40185.fa --refList OceanDNA-b40185/target_genomes.txt --output OceanDNA-b40185/fastani_result.tsv --threads 1
[2023-03-18 01:44:19,113] [INFO] Task succeeded: fastANI
[2023-03-18 01:44:19,113] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2923a629-87bb-47a9-9b91-cc6b4cd29399/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:44:19,113] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2923a629-87bb-47a9-9b91-cc6b4cd29399/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:44:19,113] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:44:19,113] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 01:44:19,113] [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
--------------------------------------------------------------------------------
[2023-03-18 01:44:19,117] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40185/tc_result.tsv
[2023-03-18 01:44:19,118] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:44:19,118] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:44:19,118] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2923a629-87bb-47a9-9b91-cc6b4cd29399/dqc_reference/checkm_data
[2023-03-18 01:44:19,121] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:44:19,127] [INFO] Task started: CheckM
[2023-03-18 01:44:19,127] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40185/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40185/checkm_input OceanDNA-b40185/checkm_result
[2023-03-18 01:44:58,824] [INFO] Task succeeded: CheckM
[2023-03-18 01:44:58,825] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 01:44:58,848] [INFO] ===== Completeness check finished =====
[2023-03-18 01:44:58,848] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:44:58,848] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40185/markers.fasta)
[2023-03-18 01:44:58,849] [INFO] Task started: Blastn
[2023-03-18 01:44:58,850] [INFO] Running command: blastn -query OceanDNA-b40185/markers.fasta -db /var/lib/cwl/stg2923a629-87bb-47a9-9b91-cc6b4cd29399/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40185/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:44:59,891] [INFO] Task succeeded: Blastn
[2023-03-18 01:44:59,896] [INFO] Selected 20 target genomes.
[2023-03-18 01:44:59,896] [INFO] Target genome list was writen to OceanDNA-b40185/target_genomes_gtdb.txt
[2023-03-18 01:45:00,011] [INFO] Task started: fastANI
[2023-03-18 01:45:00,012] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c5b6633-cc83-42ac-aa87-6b6c91bfdf0d/OceanDNA-b40185.fa --refList OceanDNA-b40185/target_genomes_gtdb.txt --output OceanDNA-b40185/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:45:09,912] [INFO] Task succeeded: fastANI
[2023-03-18 01:45:09,914] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 01:45:09,914] [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_002339165.1	s__TMED48 sp002339165	99.5785	684	827	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__TMED48	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_905181995.1	s__TMED48 sp905181995	91.773	501	827	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__TMED48	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 01:45:09,918] [INFO] GTDB search result was written to OceanDNA-b40185/result_gtdb.tsv
[2023-03-18 01:45:09,924] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:45:09,927] [INFO] DFAST_QC result json was written to OceanDNA-b40185/dqc_result.json
[2023-03-18 01:45:09,927] [INFO] DFAST_QC completed!
[2023-03-18 01:45:09,927] [INFO] Total running time: 0h1m24s