[2023-03-15 07:25:31,265] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:25:31,266] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:25:31,266] [INFO] DQC Reference Directory: /var/lib/cwl/stgfe05d30f-850f-448b-878f-3f7cb93bdc50/dqc_reference
[2023-03-15 07:25:32,936] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:25:32,937] [INFO] Task started: Prodigal
[2023-03-15 07:25:32,937] [INFO] Running command: cat /var/lib/cwl/stg8f1d7cb4-1e64-48ff-8c74-c1e3984e37a1/OceanDNA-b23169.fa | prodigal -d OceanDNA-b23169/cds.fna -a OceanDNA-b23169/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:25:45,722] [INFO] Task succeeded: Prodigal
[2023-03-15 07:25:45,723] [INFO] Task started: HMMsearch
[2023-03-15 07:25:45,723] [INFO] Running command: hmmsearch --tblout OceanDNA-b23169/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfe05d30f-850f-448b-878f-3f7cb93bdc50/dqc_reference/reference_markers.hmm OceanDNA-b23169/protein.faa > /dev/null
[2023-03-15 07:25:45,930] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:25:45,930] [INFO] Found 6/6 markers.
[2023-03-15 07:25:45,959] [INFO] Query marker FASTA was written to OceanDNA-b23169/markers.fasta
[2023-03-15 07:25:45,959] [INFO] Task started: Blastn
[2023-03-15 07:25:45,959] [INFO] Running command: blastn -query OceanDNA-b23169/markers.fasta -db /var/lib/cwl/stgfe05d30f-850f-448b-878f-3f7cb93bdc50/dqc_reference/reference_markers.fasta -out OceanDNA-b23169/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:25:46,536] [INFO] Task succeeded: Blastn
[2023-03-15 07:25:46,541] [INFO] Selected 21 target genomes.
[2023-03-15 07:25:46,541] [INFO] Target genome list was writen to OceanDNA-b23169/target_genomes.txt
[2023-03-15 07:25:46,552] [INFO] Task started: fastANI
[2023-03-15 07:25:46,552] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f1d7cb4-1e64-48ff-8c74-c1e3984e37a1/OceanDNA-b23169.fa --refList OceanDNA-b23169/target_genomes.txt --output OceanDNA-b23169/fastani_result.tsv --threads 1
[2023-03-15 07:26:00,732] [INFO] Task succeeded: fastANI
[2023-03-15 07:26:00,733] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfe05d30f-850f-448b-878f-3f7cb93bdc50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:26:00,733] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfe05d30f-850f-448b-878f-3f7cb93bdc50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:26:00,733] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:26:00,733] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 07:26:00,733] [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
--------------------------------------------------------------------------------
[2023-03-15 07:26:00,735] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23169/tc_result.tsv
[2023-03-15 07:26:00,739] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:26:00,739] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:26:00,739] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfe05d30f-850f-448b-878f-3f7cb93bdc50/dqc_reference/checkm_data
[2023-03-15 07:26:00,742] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:26:00,785] [INFO] Task started: CheckM
[2023-03-15 07:26:00,785] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23169/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23169/checkm_input OceanDNA-b23169/checkm_result
[2023-03-15 07:26:36,314] [INFO] Task succeeded: CheckM
[2023-03-15 07:26:36,315] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.33%
Contamintation: 5.09%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-03-15 07:26:36,408] [INFO] ===== Completeness check finished =====
[2023-03-15 07:26:36,408] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:26:36,408] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23169/markers.fasta)
[2023-03-15 07:26:36,409] [INFO] Task started: Blastn
[2023-03-15 07:26:36,409] [INFO] Running command: blastn -query OceanDNA-b23169/markers.fasta -db /var/lib/cwl/stgfe05d30f-850f-448b-878f-3f7cb93bdc50/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23169/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:26:37,363] [INFO] Task succeeded: Blastn
[2023-03-15 07:26:37,370] [INFO] Selected 22 target genomes.
[2023-03-15 07:26:37,371] [INFO] Target genome list was writen to OceanDNA-b23169/target_genomes_gtdb.txt
[2023-03-15 07:26:37,391] [INFO] Task started: fastANI
[2023-03-15 07:26:37,391] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f1d7cb4-1e64-48ff-8c74-c1e3984e37a1/OceanDNA-b23169.fa --refList OceanDNA-b23169/target_genomes_gtdb.txt --output OceanDNA-b23169/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:26:51,025] [INFO] Task succeeded: fastANI
[2023-03-15 07:26:51,028] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 07:26:51,028] [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_002708465.1	s__UBA8108 sp002708465	97.3276	444	660	d__Bacteria;p__Planctomycetota;c__UBA8108;o__UBA8108;f__UBA8108;g__UBA8108	95.0	95.06	95.06	0.65	0.65	2	conclusive
GCA_002320775.1	s__UBA8108 sp002320775	91.5208	610	660	d__Bacteria;p__Planctomycetota;c__UBA8108;o__UBA8108;f__UBA8108;g__UBA8108	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002695115.1	s__UBA8108 sp002695115	80.7223	364	660	d__Bacteria;p__Planctomycetota;c__UBA8108;o__UBA8108;f__UBA8108;g__UBA8108	95.0	98.97	98.97	0.70	0.70	2	-
--------------------------------------------------------------------------------
[2023-03-15 07:26:51,034] [INFO] GTDB search result was written to OceanDNA-b23169/result_gtdb.tsv
[2023-03-15 07:26:51,045] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:26:51,051] [INFO] DFAST_QC result json was written to OceanDNA-b23169/dqc_result.json
[2023-03-15 07:26:51,051] [INFO] DFAST_QC completed!
[2023-03-15 07:26:51,052] [INFO] Total running time: 0h1m20s