[2023-03-16 08:50:59,655] [INFO] DFAST_QC pipeline started.
[2023-03-16 08:50:59,655] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 08:50:59,655] [INFO] DQC Reference Directory: /var/lib/cwl/stg47de4ec6-d824-48cf-8c05-5a655a903d1c/dqc_reference
[2023-03-16 08:51:00,767] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 08:51:00,767] [INFO] Task started: Prodigal
[2023-03-16 08:51:00,767] [INFO] Running command: cat /var/lib/cwl/stg675d41c1-3224-4e28-95c9-fef0677784a3/OceanDNA-a1917.fa | prodigal -d OceanDNA-a1917/cds.fna -a OceanDNA-a1917/protein.faa -g 11 -q > /dev/null
[2023-03-16 08:51:06,089] [INFO] Task succeeded: Prodigal
[2023-03-16 08:51:06,089] [INFO] Task started: HMMsearch
[2023-03-16 08:51:06,089] [INFO] Running command: hmmsearch --tblout OceanDNA-a1917/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg47de4ec6-d824-48cf-8c05-5a655a903d1c/dqc_reference/reference_markers.hmm OceanDNA-a1917/protein.faa > /dev/null
[2023-03-16 08:51:06,246] [INFO] Task succeeded: HMMsearch
[2023-03-16 08:51:06,247] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg675d41c1-3224-4e28-95c9-fef0677784a3/OceanDNA-a1917.fa]
[2023-03-16 08:51:06,259] [INFO] Query marker FASTA was written to OceanDNA-a1917/markers.fasta
[2023-03-16 08:51:06,261] [INFO] Task started: Blastn
[2023-03-16 08:51:06,261] [INFO] Running command: blastn -query OceanDNA-a1917/markers.fasta -db /var/lib/cwl/stg47de4ec6-d824-48cf-8c05-5a655a903d1c/dqc_reference/reference_markers.fasta -out OceanDNA-a1917/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:51:06,717] [INFO] Task succeeded: Blastn
[2023-03-16 08:51:06,718] [INFO] Selected 1 target genomes.
[2023-03-16 08:51:06,719] [INFO] Target genome list was writen to OceanDNA-a1917/target_genomes.txt
[2023-03-16 08:51:06,720] [INFO] Task started: fastANI
[2023-03-16 08:51:06,720] [INFO] Running command: fastANI --query /var/lib/cwl/stg675d41c1-3224-4e28-95c9-fef0677784a3/OceanDNA-a1917.fa --refList OceanDNA-a1917/target_genomes.txt --output OceanDNA-a1917/fastani_result.tsv --threads 1
[2023-03-16 08:51:07,152] [INFO] Task succeeded: fastANI
[2023-03-16 08:51:07,153] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg47de4ec6-d824-48cf-8c05-5a655a903d1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 08:51:07,153] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg47de4ec6-d824-48cf-8c05-5a655a903d1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 08:51:07,153] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 08:51:07,153] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 08:51:07,153] [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 08:51:07,155] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1917/tc_result.tsv
[2023-03-16 08:51:07,156] [INFO] ===== Taxonomy check completed =====
[2023-03-16 08:51:07,156] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 08:51:07,156] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg47de4ec6-d824-48cf-8c05-5a655a903d1c/dqc_reference/checkm_data
[2023-03-16 08:51:07,161] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 08:51:07,164] [INFO] Task started: CheckM
[2023-03-16 08:51:07,164] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1917/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1917/checkm_input OceanDNA-a1917/checkm_result
[2023-03-16 08:51:27,209] [INFO] Task succeeded: CheckM
[2023-03-16 08:51:27,210] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.30%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 08:51:27,213] [INFO] ===== Completeness check finished =====
[2023-03-16 08:51:27,213] [INFO] ===== Start GTDB Search =====
[2023-03-16 08:51:27,213] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1917/markers.fasta)
[2023-03-16 08:51:27,216] [INFO] Task started: Blastn
[2023-03-16 08:51:27,216] [INFO] Running command: blastn -query OceanDNA-a1917/markers.fasta -db /var/lib/cwl/stg47de4ec6-d824-48cf-8c05-5a655a903d1c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1917/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:51:27,790] [INFO] Task succeeded: Blastn
[2023-03-16 08:51:27,794] [INFO] Selected 12 target genomes.
[2023-03-16 08:51:27,794] [INFO] Target genome list was writen to OceanDNA-a1917/target_genomes_gtdb.txt
[2023-03-16 08:51:27,812] [INFO] Task started: fastANI
[2023-03-16 08:51:27,813] [INFO] Running command: fastANI --query /var/lib/cwl/stg675d41c1-3224-4e28-95c9-fef0677784a3/OceanDNA-a1917.fa --refList OceanDNA-a1917/target_genomes_gtdb.txt --output OceanDNA-a1917/fastani_result_gtdb.tsv --threads 1
[2023-03-16 08:51:31,144] [INFO] Task succeeded: fastANI
[2023-03-16 08:51:31,148] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 08:51:31,148] [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_018650165.1	s__MGIIa-K1 sp018650165	78.555	148	289	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	99.75	99.69	0.90	0.90	3	-
GCA_902605365.1	s__MGIIa-K1 sp902605365	78.4609	107	289	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003602415.1	s__MGIIa-K1 sp003602415	77.3993	118	289	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	97.94	97.94	0.93	0.93	2	-
GCA_002709705.1	s__MGIIa-K1 sp002709705	76.8042	70	289	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002727695.1	s__MGIIa-K1 sp002727695	76.4948	61	289	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 08:51:31,149] [INFO] GTDB search result was written to OceanDNA-a1917/result_gtdb.tsv
[2023-03-16 08:51:31,150] [INFO] ===== GTDB Search completed =====
[2023-03-16 08:51:31,153] [INFO] DFAST_QC result json was written to OceanDNA-a1917/dqc_result.json
[2023-03-16 08:51:31,153] [INFO] DFAST_QC completed!
[2023-03-16 08:51:31,153] [INFO] Total running time: 0h0m31s