[2023-03-17 23:06:28,995] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:06:28,995] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:06:28,995] [INFO] DQC Reference Directory: /var/lib/cwl/stg91cdc69f-f2d7-4158-90cb-5288b81d6115/dqc_reference
[2023-03-17 23:06:30,114] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:06:30,115] [INFO] Task started: Prodigal
[2023-03-17 23:06:30,115] [INFO] Running command: cat /var/lib/cwl/stgb895fd24-3ad2-4e6a-83c2-be8636fa4ff0/OceanDNA-b24219.fa | prodigal -d OceanDNA-b24219/cds.fna -a OceanDNA-b24219/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:06:42,276] [INFO] Task succeeded: Prodigal
[2023-03-17 23:06:42,276] [INFO] Task started: HMMsearch
[2023-03-17 23:06:42,276] [INFO] Running command: hmmsearch --tblout OceanDNA-b24219/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg91cdc69f-f2d7-4158-90cb-5288b81d6115/dqc_reference/reference_markers.hmm OceanDNA-b24219/protein.faa > /dev/null
[2023-03-17 23:06:42,462] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:06:42,462] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb895fd24-3ad2-4e6a-83c2-be8636fa4ff0/OceanDNA-b24219.fa]
[2023-03-17 23:06:42,483] [INFO] Query marker FASTA was written to OceanDNA-b24219/markers.fasta
[2023-03-17 23:06:42,484] [INFO] Task started: Blastn
[2023-03-17 23:06:42,484] [INFO] Running command: blastn -query OceanDNA-b24219/markers.fasta -db /var/lib/cwl/stg91cdc69f-f2d7-4158-90cb-5288b81d6115/dqc_reference/reference_markers.fasta -out OceanDNA-b24219/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:06:43,128] [INFO] Task succeeded: Blastn
[2023-03-17 23:06:43,129] [INFO] Selected 29 target genomes.
[2023-03-17 23:06:43,129] [INFO] Target genome list was writen to OceanDNA-b24219/target_genomes.txt
[2023-03-17 23:06:43,146] [INFO] Task started: fastANI
[2023-03-17 23:06:43,146] [INFO] Running command: fastANI --query /var/lib/cwl/stgb895fd24-3ad2-4e6a-83c2-be8636fa4ff0/OceanDNA-b24219.fa --refList OceanDNA-b24219/target_genomes.txt --output OceanDNA-b24219/fastani_result.tsv --threads 1
[2023-03-17 23:07:00,972] [INFO] Task succeeded: fastANI
[2023-03-17 23:07:00,973] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg91cdc69f-f2d7-4158-90cb-5288b81d6115/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:07:00,973] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg91cdc69f-f2d7-4158-90cb-5288b81d6115/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:07:00,973] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:07:00,973] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 23:07:00,973] [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
--------------------------------------------------------------------------------
[2023-03-17 23:07:00,973] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24219/tc_result.tsv
[2023-03-17 23:07:00,973] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:07:00,973] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:07:00,973] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg91cdc69f-f2d7-4158-90cb-5288b81d6115/dqc_reference/checkm_data
[2023-03-17 23:07:01,051] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:07:01,056] [INFO] Task started: CheckM
[2023-03-17 23:07:01,056] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24219/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24219/checkm_input OceanDNA-b24219/checkm_result
[2023-03-17 23:07:35,927] [INFO] Task succeeded: CheckM
[2023-03-17 23:07:35,927] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.49%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 23:07:35,930] [INFO] ===== Completeness check finished =====
[2023-03-17 23:07:35,930] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:07:35,930] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24219/markers.fasta)
[2023-03-17 23:07:35,931] [INFO] Task started: Blastn
[2023-03-17 23:07:35,931] [INFO] Running command: blastn -query OceanDNA-b24219/markers.fasta -db /var/lib/cwl/stg91cdc69f-f2d7-4158-90cb-5288b81d6115/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24219/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:07:37,001] [INFO] Task succeeded: Blastn
[2023-03-17 23:07:37,002] [INFO] Selected 19 target genomes.
[2023-03-17 23:07:37,002] [INFO] Target genome list was writen to OceanDNA-b24219/target_genomes_gtdb.txt
[2023-03-17 23:07:37,017] [INFO] Task started: fastANI
[2023-03-17 23:07:37,017] [INFO] Running command: fastANI --query /var/lib/cwl/stgb895fd24-3ad2-4e6a-83c2-be8636fa4ff0/OceanDNA-b24219.fa --refList OceanDNA-b24219/target_genomes_gtdb.txt --output OceanDNA-b24219/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:07:48,671] [INFO] Task succeeded: fastANI
[2023-03-17 23:07:48,673] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 23:07:48,673] [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_018666155.1	s__WLXB01 sp018666155	99.8933	636	640	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__WLXB01	95.0	99.93	99.91	0.96	0.93	5	conclusive
GCA_012103295.1	s__WLXB01 sp012103295	80.2781	448	640	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__WLXB01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 23:07:48,673] [INFO] GTDB search result was written to OceanDNA-b24219/result_gtdb.tsv
[2023-03-17 23:07:48,673] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:07:48,674] [INFO] DFAST_QC result json was written to OceanDNA-b24219/dqc_result.json
[2023-03-17 23:07:48,674] [INFO] DFAST_QC completed!
[2023-03-17 23:07:48,674] [INFO] Total running time: 0h1m20s