[2023-03-15 10:21:46,237] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:21:46,237] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:21:46,237] [INFO] DQC Reference Directory: /var/lib/cwl/stg20b3e438-aa96-44fa-bdc9-ea1dad7c7258/dqc_reference
[2023-03-15 10:21:47,931] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:21:47,935] [INFO] Task started: Prodigal
[2023-03-15 10:21:47,935] [INFO] Running command: cat /var/lib/cwl/stgccca7a4a-9d8c-4e4f-93a6-a6593e4189cc/OceanDNA-a1549.fa | prodigal -d OceanDNA-a1549/cds.fna -a OceanDNA-a1549/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:21:52,198] [INFO] Task succeeded: Prodigal
[2023-03-15 10:21:52,198] [INFO] Task started: HMMsearch
[2023-03-15 10:21:52,198] [INFO] Running command: hmmsearch --tblout OceanDNA-a1549/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg20b3e438-aa96-44fa-bdc9-ea1dad7c7258/dqc_reference/reference_markers.hmm OceanDNA-a1549/protein.faa > /dev/null
[2023-03-15 10:21:52,368] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:21:52,368] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgccca7a4a-9d8c-4e4f-93a6-a6593e4189cc/OceanDNA-a1549.fa]
[2023-03-15 10:21:52,376] [INFO] Query marker FASTA was written to OceanDNA-a1549/markers.fasta
[2023-03-15 10:21:52,377] [INFO] Task started: Blastn
[2023-03-15 10:21:52,377] [INFO] Running command: blastn -query OceanDNA-a1549/markers.fasta -db /var/lib/cwl/stg20b3e438-aa96-44fa-bdc9-ea1dad7c7258/dqc_reference/reference_markers.fasta -out OceanDNA-a1549/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:21:53,771] [INFO] Task succeeded: Blastn
[2023-03-15 10:21:53,771] [INFO] Selected 5 target genomes.
[2023-03-15 10:21:53,772] [INFO] Target genome list was writen to OceanDNA-a1549/target_genomes.txt
[2023-03-15 10:21:53,775] [INFO] Task started: fastANI
[2023-03-15 10:21:53,776] [INFO] Running command: fastANI --query /var/lib/cwl/stgccca7a4a-9d8c-4e4f-93a6-a6593e4189cc/OceanDNA-a1549.fa --refList OceanDNA-a1549/target_genomes.txt --output OceanDNA-a1549/fastani_result.tsv --threads 1
[2023-03-15 10:21:56,856] [INFO] Task succeeded: fastANI
[2023-03-15 10:21:56,857] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg20b3e438-aa96-44fa-bdc9-ea1dad7c7258/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:21:56,857] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg20b3e438-aa96-44fa-bdc9-ea1dad7c7258/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:21:56,857] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:21:56,857] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 10:21:56,857] [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 10:21:56,858] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1549/tc_result.tsv
[2023-03-15 10:21:56,858] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:21:56,858] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:21:56,858] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg20b3e438-aa96-44fa-bdc9-ea1dad7c7258/dqc_reference/checkm_data
[2023-03-15 10:21:56,860] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:21:56,863] [INFO] Task started: CheckM
[2023-03-15 10:21:56,863] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1549/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1549/checkm_input OceanDNA-a1549/checkm_result
[2023-03-15 10:22:15,240] [INFO] Task succeeded: CheckM
[2023-03-15 10:22:15,240] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 1.39%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 10:22:15,242] [INFO] ===== Completeness check finished =====
[2023-03-15 10:22:15,242] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:22:15,242] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1549/markers.fasta)
[2023-03-15 10:22:15,242] [INFO] Task started: Blastn
[2023-03-15 10:22:15,242] [INFO] Running command: blastn -query OceanDNA-a1549/markers.fasta -db /var/lib/cwl/stg20b3e438-aa96-44fa-bdc9-ea1dad7c7258/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1549/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:22:16,364] [INFO] Task succeeded: Blastn
[2023-03-15 10:22:16,365] [INFO] Selected 8 target genomes.
[2023-03-15 10:22:16,365] [INFO] Target genome list was writen to OceanDNA-a1549/target_genomes_gtdb.txt
[2023-03-15 10:22:16,669] [INFO] Task started: fastANI
[2023-03-15 10:22:16,669] [INFO] Running command: fastANI --query /var/lib/cwl/stgccca7a4a-9d8c-4e4f-93a6-a6593e4189cc/OceanDNA-a1549.fa --refList OceanDNA-a1549/target_genomes_gtdb.txt --output OceanDNA-a1549/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:22:18,238] [INFO] Task succeeded: fastANI
[2023-03-15 10:22:18,243] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 10:22:18,244] [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_014240055.1	s__CG-Epi1 sp014240055	87.2532	213	267	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014240255.1	s__CG-Epi1 sp014240255	84.7845	220	267	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902533295.1	s__CG-Epi1 sp902533295	78.4501	71	267	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902531985.1	s__CG-Epi1 sp902531985	77.6337	73	267	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001875345.1	s__CG-Epi1 sp001875345	77.4323	69	267	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002718915.1	s__CG-Epi1 sp002718915	77.2462	52	267	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016845825.1	s__CG-Epi1 sp016845825	77.0671	64	267	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 10:22:18,244] [INFO] GTDB search result was written to OceanDNA-a1549/result_gtdb.tsv
[2023-03-15 10:22:18,244] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:22:18,245] [INFO] DFAST_QC result json was written to OceanDNA-a1549/dqc_result.json
[2023-03-15 10:22:18,245] [INFO] DFAST_QC completed!
[2023-03-15 10:22:18,245] [INFO] Total running time: 0h0m32s