[2023-03-15 08:09:45,341] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:09:45,341] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:09:45,341] [INFO] DQC Reference Directory: /var/lib/cwl/stg5086fec9-9702-4a91-a25d-09f72f413e34/dqc_reference
[2023-03-15 08:09:46,593] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:09:46,594] [INFO] Task started: Prodigal
[2023-03-15 08:09:46,594] [INFO] Running command: cat /var/lib/cwl/stga8b0f0a9-0ca5-431d-9ac5-146d3b105582/OceanDNA-a1590.fa | prodigal -d OceanDNA-a1590/cds.fna -a OceanDNA-a1590/protein.faa -g 11 -q > /dev/null
[2023-03-15 08:09:49,860] [INFO] Task succeeded: Prodigal
[2023-03-15 08:09:49,860] [INFO] Task started: HMMsearch
[2023-03-15 08:09:49,861] [INFO] Running command: hmmsearch --tblout OceanDNA-a1590/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5086fec9-9702-4a91-a25d-09f72f413e34/dqc_reference/reference_markers.hmm OceanDNA-a1590/protein.faa > /dev/null
[2023-03-15 08:09:50,051] [INFO] Task succeeded: HMMsearch
[2023-03-15 08:09:50,052] [WARNING] Found 3/6 markers. [/var/lib/cwl/stga8b0f0a9-0ca5-431d-9ac5-146d3b105582/OceanDNA-a1590.fa]
[2023-03-15 08:09:50,059] [INFO] Query marker FASTA was written to OceanDNA-a1590/markers.fasta
[2023-03-15 08:09:50,059] [INFO] Task started: Blastn
[2023-03-15 08:09:50,059] [INFO] Running command: blastn -query OceanDNA-a1590/markers.fasta -db /var/lib/cwl/stg5086fec9-9702-4a91-a25d-09f72f413e34/dqc_reference/reference_markers.fasta -out OceanDNA-a1590/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:09:50,580] [INFO] Task succeeded: Blastn
[2023-03-15 08:09:50,581] [INFO] Selected 5 target genomes.
[2023-03-15 08:09:50,581] [INFO] Target genome list was writen to OceanDNA-a1590/target_genomes.txt
[2023-03-15 08:09:50,586] [INFO] Task started: fastANI
[2023-03-15 08:09:50,586] [INFO] Running command: fastANI --query /var/lib/cwl/stga8b0f0a9-0ca5-431d-9ac5-146d3b105582/OceanDNA-a1590.fa --refList OceanDNA-a1590/target_genomes.txt --output OceanDNA-a1590/fastani_result.tsv --threads 1
[2023-03-15 08:09:53,852] [INFO] Task succeeded: fastANI
[2023-03-15 08:09:53,852] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5086fec9-9702-4a91-a25d-09f72f413e34/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 08:09:53,853] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5086fec9-9702-4a91-a25d-09f72f413e34/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 08:09:53,853] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 08:09:53,853] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 08:09:53,853] [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 08:09:53,853] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1590/tc_result.tsv
[2023-03-15 08:09:53,853] [INFO] ===== Taxonomy check completed =====
[2023-03-15 08:09:53,853] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 08:09:53,853] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5086fec9-9702-4a91-a25d-09f72f413e34/dqc_reference/checkm_data
[2023-03-15 08:09:53,856] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 08:09:54,150] [INFO] Task started: CheckM
[2023-03-15 08:09:54,150] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1590/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1590/checkm_input OceanDNA-a1590/checkm_result
[2023-03-15 08:10:09,177] [INFO] Task succeeded: CheckM
[2023-03-15 08:10:09,177] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 08:10:09,179] [INFO] ===== Completeness check finished =====
[2023-03-15 08:10:09,179] [INFO] ===== Start GTDB Search =====
[2023-03-15 08:10:09,179] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1590/markers.fasta)
[2023-03-15 08:10:09,180] [INFO] Task started: Blastn
[2023-03-15 08:10:09,180] [INFO] Running command: blastn -query OceanDNA-a1590/markers.fasta -db /var/lib/cwl/stg5086fec9-9702-4a91-a25d-09f72f413e34/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1590/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:10:09,869] [INFO] Task succeeded: Blastn
[2023-03-15 08:10:09,870] [INFO] Selected 10 target genomes.
[2023-03-15 08:10:09,870] [INFO] Target genome list was writen to OceanDNA-a1590/target_genomes_gtdb.txt
[2023-03-15 08:10:09,879] [INFO] Task started: fastANI
[2023-03-15 08:10:09,879] [INFO] Running command: fastANI --query /var/lib/cwl/stga8b0f0a9-0ca5-431d-9ac5-146d3b105582/OceanDNA-a1590.fa --refList OceanDNA-a1590/target_genomes_gtdb.txt --output OceanDNA-a1590/fastani_result_gtdb.tsv --threads 1
[2023-03-15 08:10:11,885] [INFO] Task succeeded: fastANI
[2023-03-15 08:10:11,892] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 08:10:11,892] [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_902533295.1	s__CG-Epi1 sp902533295	80.769	90	205	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	78.996	69	205	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	78.6064	108	205	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_902627615.1	s__CG-Epi1 sp902627615	78.4547	101	205	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_002506485.1	s__CG-Epi1 sp002506485	78.0198	60	205	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	99.64	99.58	0.87	0.83	4	-
GCA_014240055.1	s__CG-Epi1 sp014240055	78.0162	93	205	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	77.1573	57	205	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	76.946	51	205	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_002497685.1	s__CG-Epi1 sp002497685	76.7491	56	205	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__MGIII;f__CG-Epi1;g__CG-Epi1	95.0	99.79	99.79	0.70	0.70	2	-
--------------------------------------------------------------------------------
[2023-03-15 08:10:11,892] [INFO] GTDB search result was written to OceanDNA-a1590/result_gtdb.tsv
[2023-03-15 08:10:11,892] [INFO] ===== GTDB Search completed =====
[2023-03-15 08:10:11,893] [INFO] DFAST_QC result json was written to OceanDNA-a1590/dqc_result.json
[2023-03-15 08:10:11,893] [INFO] DFAST_QC completed!
[2023-03-15 08:10:11,893] [INFO] Total running time: 0h0m27s