[2023-03-16 07:28:30,040] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:28:30,040] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:28:30,040] [INFO] DQC Reference Directory: /var/lib/cwl/stg774353d7-0abf-46b7-a992-94b02c43f030/dqc_reference
[2023-03-16 07:28:31,157] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:28:31,158] [INFO] Task started: Prodigal
[2023-03-16 07:28:31,158] [INFO] Running command: cat /var/lib/cwl/stg1d17eb0a-7d2d-4473-b615-a6ecb8b5cee3/OceanDNA-a3203.fa | prodigal -d OceanDNA-a3203/cds.fna -a OceanDNA-a3203/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:28:37,220] [INFO] Task succeeded: Prodigal
[2023-03-16 07:28:37,220] [INFO] Task started: HMMsearch
[2023-03-16 07:28:37,220] [INFO] Running command: hmmsearch --tblout OceanDNA-a3203/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg774353d7-0abf-46b7-a992-94b02c43f030/dqc_reference/reference_markers.hmm OceanDNA-a3203/protein.faa > /dev/null
[2023-03-16 07:28:37,382] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:28:37,383] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg1d17eb0a-7d2d-4473-b615-a6ecb8b5cee3/OceanDNA-a3203.fa]
[2023-03-16 07:28:37,397] [INFO] Query marker FASTA was written to OceanDNA-a3203/markers.fasta
[2023-03-16 07:28:37,398] [INFO] Task started: Blastn
[2023-03-16 07:28:37,398] [INFO] Running command: blastn -query OceanDNA-a3203/markers.fasta -db /var/lib/cwl/stg774353d7-0abf-46b7-a992-94b02c43f030/dqc_reference/reference_markers.fasta -out OceanDNA-a3203/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:28:37,844] [INFO] Task succeeded: Blastn
[2023-03-16 07:28:37,846] [INFO] Selected 6 target genomes.
[2023-03-16 07:28:37,846] [INFO] Target genome list was writen to OceanDNA-a3203/target_genomes.txt
[2023-03-16 07:28:37,852] [INFO] Task started: fastANI
[2023-03-16 07:28:37,852] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d17eb0a-7d2d-4473-b615-a6ecb8b5cee3/OceanDNA-a3203.fa --refList OceanDNA-a3203/target_genomes.txt --output OceanDNA-a3203/fastani_result.tsv --threads 1
[2023-03-16 07:28:41,222] [INFO] Task succeeded: fastANI
[2023-03-16 07:28:41,222] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg774353d7-0abf-46b7-a992-94b02c43f030/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:28:41,222] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg774353d7-0abf-46b7-a992-94b02c43f030/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:28:41,222] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 07:28:41,222] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 07:28:41,222] [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
--------------------------------------------------------------------------------
[2023-03-16 07:28:41,223] [INFO] DFAST Taxonomy check result was written to OceanDNA-a3203/tc_result.tsv
[2023-03-16 07:28:41,224] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:28:41,224] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:28:41,224] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg774353d7-0abf-46b7-a992-94b02c43f030/dqc_reference/checkm_data
[2023-03-16 07:28:41,280] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:28:41,795] [INFO] Task started: CheckM
[2023-03-16 07:28:41,795] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a3203/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a3203/checkm_input OceanDNA-a3203/checkm_result
[2023-03-16 07:29:03,352] [INFO] Task succeeded: CheckM
[2023-03-16 07:29:03,352] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.10%
Contamintation: 1.50%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-16 07:29:03,355] [INFO] ===== Completeness check finished =====
[2023-03-16 07:29:03,355] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:29:03,355] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a3203/markers.fasta)
[2023-03-16 07:29:03,356] [INFO] Task started: Blastn
[2023-03-16 07:29:03,356] [INFO] Running command: blastn -query OceanDNA-a3203/markers.fasta -db /var/lib/cwl/stg774353d7-0abf-46b7-a992-94b02c43f030/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a3203/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:29:03,790] [INFO] Task succeeded: Blastn
[2023-03-16 07:29:03,791] [INFO] Selected 8 target genomes.
[2023-03-16 07:29:03,791] [INFO] Target genome list was writen to OceanDNA-a3203/target_genomes_gtdb.txt
[2023-03-16 07:29:03,962] [INFO] Task started: fastANI
[2023-03-16 07:29:03,962] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d17eb0a-7d2d-4473-b615-a6ecb8b5cee3/OceanDNA-a3203.fa --refList OceanDNA-a3203/target_genomes_gtdb.txt --output OceanDNA-a3203/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:29:06,648] [INFO] Task succeeded: fastANI
[2023-03-16 07:29:06,652] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 07:29:06,652] [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_014384685.1	s__MGIIb-Q1 sp014384685	95.67	194	301	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-Q1	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016845345.1	s__MGIIb-Q1 sp016845345	89.673	282	301	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-Q1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012959435.1	s__MGIIb-Q1 sp012959435	86.7121	278	301	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-Q1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012964335.1	s__MGIIb-Q1 sp012964335	85.6544	272	301	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-Q1	95.0	99.77	99.71	0.95	0.94	8	-
GCA_018650285.1	s__MGIIb-Q1 sp018650285	78.8622	127	301	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-Q1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 07:29:06,653] [INFO] GTDB search result was written to OceanDNA-a3203/result_gtdb.tsv
[2023-03-16 07:29:06,653] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:29:06,653] [INFO] DFAST_QC result json was written to OceanDNA-a3203/dqc_result.json
[2023-03-16 07:29:06,654] [INFO] DFAST_QC completed!
[2023-03-16 07:29:06,654] [INFO] Total running time: 0h0m37s