[2023-03-16 23:35:12,973] [INFO] DFAST_QC pipeline started.
[2023-03-16 23:35:12,973] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 23:35:12,973] [INFO] DQC Reference Directory: /var/lib/cwl/stge6175bb3-b17b-4491-a999-b266dac17ffc/dqc_reference
[2023-03-16 23:35:14,100] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 23:35:14,100] [INFO] Task started: Prodigal
[2023-03-16 23:35:14,100] [INFO] Running command: cat /var/lib/cwl/stg99c062b9-f106-4c3f-9c91-a4af5228f793/OceanDNA-a3215.fa | prodigal -d OceanDNA-a3215/cds.fna -a OceanDNA-a3215/protein.faa -g 11 -q > /dev/null
[2023-03-16 23:35:20,690] [INFO] Task succeeded: Prodigal
[2023-03-16 23:35:20,691] [INFO] Task started: HMMsearch
[2023-03-16 23:35:20,691] [INFO] Running command: hmmsearch --tblout OceanDNA-a3215/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge6175bb3-b17b-4491-a999-b266dac17ffc/dqc_reference/reference_markers.hmm OceanDNA-a3215/protein.faa > /dev/null
[2023-03-16 23:35:20,850] [INFO] Task succeeded: HMMsearch
[2023-03-16 23:35:20,851] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg99c062b9-f106-4c3f-9c91-a4af5228f793/OceanDNA-a3215.fa]
[2023-03-16 23:35:20,862] [INFO] Query marker FASTA was written to OceanDNA-a3215/markers.fasta
[2023-03-16 23:35:20,862] [INFO] Task started: Blastn
[2023-03-16 23:35:20,863] [INFO] Running command: blastn -query OceanDNA-a3215/markers.fasta -db /var/lib/cwl/stge6175bb3-b17b-4491-a999-b266dac17ffc/dqc_reference/reference_markers.fasta -out OceanDNA-a3215/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:35:21,284] [INFO] Task succeeded: Blastn
[2023-03-16 23:35:21,285] [INFO] Selected 5 target genomes.
[2023-03-16 23:35:21,285] [INFO] Target genome list was writen to OceanDNA-a3215/target_genomes.txt
[2023-03-16 23:35:21,289] [INFO] Task started: fastANI
[2023-03-16 23:35:21,289] [INFO] Running command: fastANI --query /var/lib/cwl/stg99c062b9-f106-4c3f-9c91-a4af5228f793/OceanDNA-a3215.fa --refList OceanDNA-a3215/target_genomes.txt --output OceanDNA-a3215/fastani_result.tsv --threads 1
[2023-03-16 23:35:22,811] [INFO] Task succeeded: fastANI
[2023-03-16 23:35:22,811] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge6175bb3-b17b-4491-a999-b266dac17ffc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 23:35:22,811] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge6175bb3-b17b-4491-a999-b266dac17ffc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 23:35:22,812] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 23:35:22,812] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 23:35:22,812] [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 23:35:22,812] [INFO] DFAST Taxonomy check result was written to OceanDNA-a3215/tc_result.tsv
[2023-03-16 23:35:22,812] [INFO] ===== Taxonomy check completed =====
[2023-03-16 23:35:22,812] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 23:35:22,812] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge6175bb3-b17b-4491-a999-b266dac17ffc/dqc_reference/checkm_data
[2023-03-16 23:35:22,862] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 23:35:22,865] [INFO] Task started: CheckM
[2023-03-16 23:35:22,865] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a3215/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a3215/checkm_input OceanDNA-a3215/checkm_result
[2023-03-16 23:35:46,656] [INFO] Task succeeded: CheckM
[2023-03-16 23:35:46,657] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.06%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 23:35:46,658] [INFO] ===== Completeness check finished =====
[2023-03-16 23:35:46,658] [INFO] ===== Start GTDB Search =====
[2023-03-16 23:35:46,658] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a3215/markers.fasta)
[2023-03-16 23:35:46,659] [INFO] Task started: Blastn
[2023-03-16 23:35:46,659] [INFO] Running command: blastn -query OceanDNA-a3215/markers.fasta -db /var/lib/cwl/stge6175bb3-b17b-4491-a999-b266dac17ffc/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a3215/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:35:47,329] [INFO] Task succeeded: Blastn
[2023-03-16 23:35:47,329] [INFO] Selected 12 target genomes.
[2023-03-16 23:35:47,329] [INFO] Target genome list was writen to OceanDNA-a3215/target_genomes_gtdb.txt
[2023-03-16 23:35:47,593] [INFO] Task started: fastANI
[2023-03-16 23:35:47,593] [INFO] Running command: fastANI --query /var/lib/cwl/stg99c062b9-f106-4c3f-9c91-a4af5228f793/OceanDNA-a3215.fa --refList OceanDNA-a3215/target_genomes_gtdb.txt --output OceanDNA-a3215/fastani_result_gtdb.tsv --threads 1
[2023-03-16 23:35:51,502] [INFO] Task succeeded: fastANI
[2023-03-16 23:35:51,506] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 23:35:51,507] [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_012964335.1	s__MGIIb-Q1 sp012964335	90.5146	357	389	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_012959435.1	s__MGIIb-Q1 sp012959435	85.4393	331	389	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_014384685.1	s__MGIIb-Q1 sp014384685	83.1763	221	389	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_016845345.1	s__MGIIb-Q1 sp016845345	82.1554	318	389	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_018650285.1	s__MGIIb-Q1 sp018650285	77.9696	141	389	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 23:35:51,507] [INFO] GTDB search result was written to OceanDNA-a3215/result_gtdb.tsv
[2023-03-16 23:35:51,507] [INFO] ===== GTDB Search completed =====
[2023-03-16 23:35:51,507] [INFO] DFAST_QC result json was written to OceanDNA-a3215/dqc_result.json
[2023-03-16 23:35:51,508] [INFO] DFAST_QC completed!
[2023-03-16 23:35:51,508] [INFO] Total running time: 0h0m39s