[2023-03-14 13:05:30,731] [INFO] DFAST_QC pipeline started.
[2023-03-14 13:05:30,731] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 13:05:30,731] [INFO] DQC Reference Directory: /var/lib/cwl/stg91bca7ee-1c12-4175-ae73-f9a128858cfb/dqc_reference
[2023-03-14 13:05:31,798] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 13:05:31,798] [INFO] Task started: Prodigal
[2023-03-14 13:05:31,798] [INFO] Running command: cat /var/lib/cwl/stgdb328cc7-bb2f-4ad4-944a-fd41c660c72a/OceanDNA-a5107.fa | prodigal -d OceanDNA-a5107/cds.fna -a OceanDNA-a5107/protein.faa -g 11 -q > /dev/null
[2023-03-14 13:05:39,066] [INFO] Task succeeded: Prodigal
[2023-03-14 13:05:39,066] [INFO] Task started: HMMsearch
[2023-03-14 13:05:39,066] [INFO] Running command: hmmsearch --tblout OceanDNA-a5107/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg91bca7ee-1c12-4175-ae73-f9a128858cfb/dqc_reference/reference_markers.hmm OceanDNA-a5107/protein.faa > /dev/null
[2023-03-14 13:05:39,228] [INFO] Task succeeded: HMMsearch
[2023-03-14 13:05:39,228] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgdb328cc7-bb2f-4ad4-944a-fd41c660c72a/OceanDNA-a5107.fa]
[2023-03-14 13:05:39,238] [INFO] Query marker FASTA was written to OceanDNA-a5107/markers.fasta
[2023-03-14 13:05:39,240] [INFO] Task started: Blastn
[2023-03-14 13:05:39,240] [INFO] Running command: blastn -query OceanDNA-a5107/markers.fasta -db /var/lib/cwl/stg91bca7ee-1c12-4175-ae73-f9a128858cfb/dqc_reference/reference_markers.fasta -out OceanDNA-a5107/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:05:39,711] [INFO] Task succeeded: Blastn
[2023-03-14 13:05:39,712] [INFO] Selected 5 target genomes.
[2023-03-14 13:05:39,712] [INFO] Target genome list was writen to OceanDNA-a5107/target_genomes.txt
[2023-03-14 13:05:39,715] [INFO] Task started: fastANI
[2023-03-14 13:05:39,715] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb328cc7-bb2f-4ad4-944a-fd41c660c72a/OceanDNA-a5107.fa --refList OceanDNA-a5107/target_genomes.txt --output OceanDNA-a5107/fastani_result.tsv --threads 1
[2023-03-14 13:05:42,892] [INFO] Task succeeded: fastANI
[2023-03-14 13:05:42,892] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg91bca7ee-1c12-4175-ae73-f9a128858cfb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 13:05:42,892] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg91bca7ee-1c12-4175-ae73-f9a128858cfb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 13:05:42,892] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 13:05:42,892] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 13:05:42,892] [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
--------------------------------------------------------------------------------
[2023-03-14 13:05:42,893] [INFO] DFAST Taxonomy check result was written to OceanDNA-a5107/tc_result.tsv
[2023-03-14 13:05:42,893] [INFO] ===== Taxonomy check completed =====
[2023-03-14 13:05:42,893] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 13:05:42,893] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg91bca7ee-1c12-4175-ae73-f9a128858cfb/dqc_reference/checkm_data
[2023-03-14 13:05:42,944] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 13:05:42,950] [INFO] Task started: CheckM
[2023-03-14 13:05:42,950] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a5107/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a5107/checkm_input OceanDNA-a5107/checkm_result
[2023-03-14 13:06:07,206] [INFO] Task succeeded: CheckM
[2023-03-14 13:06:07,206] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.90%
Contamintation: 0.93%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-14 13:06:07,208] [INFO] ===== Completeness check finished =====
[2023-03-14 13:06:07,208] [INFO] ===== Start GTDB Search =====
[2023-03-14 13:06:07,208] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a5107/markers.fasta)
[2023-03-14 13:06:07,210] [INFO] Task started: Blastn
[2023-03-14 13:06:07,210] [INFO] Running command: blastn -query OceanDNA-a5107/markers.fasta -db /var/lib/cwl/stg91bca7ee-1c12-4175-ae73-f9a128858cfb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a5107/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:06:07,810] [INFO] Task succeeded: Blastn
[2023-03-14 13:06:07,811] [INFO] Selected 7 target genomes.
[2023-03-14 13:06:07,811] [INFO] Target genome list was writen to OceanDNA-a5107/target_genomes_gtdb.txt
[2023-03-14 13:06:07,821] [INFO] Task started: fastANI
[2023-03-14 13:06:07,821] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb328cc7-bb2f-4ad4-944a-fd41c660c72a/OceanDNA-a5107.fa --refList OceanDNA-a5107/target_genomes_gtdb.txt --output OceanDNA-a5107/fastani_result_gtdb.tsv --threads 1
[2023-03-14 13:06:09,662] [INFO] Task succeeded: fastANI
[2023-03-14 13:06:09,666] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 13:06:09,666] [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_002507125.1	s__Thalassarchaeum sp002507125	98.4367	271	387	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	98.54	98.42	0.77	0.74	3	conclusive
GCA_003193925.1	s__Thalassarchaeum betae	84.8715	348	387	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	99.52	98.11	0.96	0.90	6	-
GCA_004195715.1	s__Thalassarchaeum sp004195715	79.8818	217	387	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	99.87	99.86	0.95	0.94	3	-
GCA_014240285.1	s__Thalassarchaeum sp014240285	79.2689	187	387	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002457605.1	s__Thalassarchaeum sp002457605	78.7962	141	387	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__Thalassarchaeum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002722735.1	s__MGIIb-O3 sp002722735	77.1702	71	387	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O3	95.0	99.60	99.54	0.93	0.90	4	-
--------------------------------------------------------------------------------
[2023-03-14 13:06:09,667] [INFO] GTDB search result was written to OceanDNA-a5107/result_gtdb.tsv
[2023-03-14 13:06:09,667] [INFO] ===== GTDB Search completed =====
[2023-03-14 13:06:09,667] [INFO] DFAST_QC result json was written to OceanDNA-a5107/dqc_result.json
[2023-03-14 13:06:09,668] [INFO] DFAST_QC completed!
[2023-03-14 13:06:09,668] [INFO] Total running time: 0h0m39s