[2023-03-17 05:01:06,438] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:01:06,438] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:01:06,439] [INFO] DQC Reference Directory: /var/lib/cwl/stgba8c8a70-96c4-46f4-9db8-30350d601fed/dqc_reference
[2023-03-17 05:01:07,999] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:01:07,999] [INFO] Task started: Prodigal
[2023-03-17 05:01:08,000] [INFO] Running command: cat /var/lib/cwl/stg7155a416-285c-4115-a0c7-3b42b2dcf07f/OceanDNA-a3696.fa | prodigal -d OceanDNA-a3696/cds.fna -a OceanDNA-a3696/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:01:13,652] [INFO] Task succeeded: Prodigal
[2023-03-17 05:01:13,652] [INFO] Task started: HMMsearch
[2023-03-17 05:01:13,652] [INFO] Running command: hmmsearch --tblout OceanDNA-a3696/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgba8c8a70-96c4-46f4-9db8-30350d601fed/dqc_reference/reference_markers.hmm OceanDNA-a3696/protein.faa > /dev/null
[2023-03-17 05:01:13,806] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:01:13,807] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg7155a416-285c-4115-a0c7-3b42b2dcf07f/OceanDNA-a3696.fa]
[2023-03-17 05:01:13,816] [INFO] Query marker FASTA was written to OceanDNA-a3696/markers.fasta
[2023-03-17 05:01:13,816] [INFO] Task started: Blastn
[2023-03-17 05:01:13,816] [INFO] Running command: blastn -query OceanDNA-a3696/markers.fasta -db /var/lib/cwl/stgba8c8a70-96c4-46f4-9db8-30350d601fed/dqc_reference/reference_markers.fasta -out OceanDNA-a3696/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:01:14,870] [INFO] Task succeeded: Blastn
[2023-03-17 05:01:14,870] [INFO] Selected 2 target genomes.
[2023-03-17 05:01:14,871] [INFO] Target genome list was writen to OceanDNA-a3696/target_genomes.txt
[2023-03-17 05:01:14,872] [INFO] Task started: fastANI
[2023-03-17 05:01:14,872] [INFO] Running command: fastANI --query /var/lib/cwl/stg7155a416-285c-4115-a0c7-3b42b2dcf07f/OceanDNA-a3696.fa --refList OceanDNA-a3696/target_genomes.txt --output OceanDNA-a3696/fastani_result.tsv --threads 1
[2023-03-17 05:01:15,537] [INFO] Task succeeded: fastANI
[2023-03-17 05:01:15,537] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgba8c8a70-96c4-46f4-9db8-30350d601fed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:01:15,537] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgba8c8a70-96c4-46f4-9db8-30350d601fed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:01:15,538] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:01:15,538] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 05:01:15,538] [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
--------------------------------------------------------------------------------
[2023-03-17 05:01:15,538] [INFO] DFAST Taxonomy check result was written to OceanDNA-a3696/tc_result.tsv
[2023-03-17 05:01:15,538] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:01:15,538] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:01:15,538] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgba8c8a70-96c4-46f4-9db8-30350d601fed/dqc_reference/checkm_data
[2023-03-17 05:01:15,592] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:01:15,595] [INFO] Task started: CheckM
[2023-03-17 05:01:15,595] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a3696/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a3696/checkm_input OceanDNA-a3696/checkm_result
[2023-03-17 05:01:37,678] [INFO] Task succeeded: CheckM
[2023-03-17 05:01:37,678] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.73%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 05:01:37,680] [INFO] ===== Completeness check finished =====
[2023-03-17 05:01:37,680] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:01:37,680] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a3696/markers.fasta)
[2023-03-17 05:01:37,681] [INFO] Task started: Blastn
[2023-03-17 05:01:37,681] [INFO] Running command: blastn -query OceanDNA-a3696/markers.fasta -db /var/lib/cwl/stgba8c8a70-96c4-46f4-9db8-30350d601fed/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a3696/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:01:38,246] [INFO] Task succeeded: Blastn
[2023-03-17 05:01:38,247] [INFO] Selected 8 target genomes.
[2023-03-17 05:01:38,247] [INFO] Target genome list was writen to OceanDNA-a3696/target_genomes_gtdb.txt
[2023-03-17 05:01:38,521] [INFO] Task started: fastANI
[2023-03-17 05:01:38,521] [INFO] Running command: fastANI --query /var/lib/cwl/stg7155a416-285c-4115-a0c7-3b42b2dcf07f/OceanDNA-a3696.fa --refList OceanDNA-a3696/target_genomes_gtdb.txt --output OceanDNA-a3696/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:01:40,242] [INFO] Task succeeded: fastANI
[2023-03-17 05:01:40,246] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 05:01:40,246] [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_013330385.1	s__MGIIb-O1 sp12570u	98.4272	218	315	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O1	95.0	100.00	100.00	0.97	0.97	2	conclusive
GCA_002457595.1	s__MGIIb-O1 sp002457595	86.6891	154	315	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002498725.1	s__MGIIb-O1 sp002498725	77.0446	56	315	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O1	95.0	99.85	99.71	0.96	0.95	4	-
GCA_002502175.1	s__MGIIb-O1 sp002502175	76.2871	61	315	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O1	95.0	98.79	95.28	0.87	0.80	11	-
--------------------------------------------------------------------------------
[2023-03-17 05:01:40,246] [INFO] GTDB search result was written to OceanDNA-a3696/result_gtdb.tsv
[2023-03-17 05:01:40,246] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:01:40,247] [INFO] DFAST_QC result json was written to OceanDNA-a3696/dqc_result.json
[2023-03-17 05:01:40,247] [INFO] DFAST_QC completed!
[2023-03-17 05:01:40,247] [INFO] Total running time: 0h0m34s