[2023-03-16 23:42:36,499] [INFO] DFAST_QC pipeline started.
[2023-03-16 23:42:36,499] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 23:42:36,499] [INFO] DQC Reference Directory: /var/lib/cwl/stg45edc875-1503-4f95-b98d-6be402b24843/dqc_reference
[2023-03-16 23:42:38,874] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 23:42:38,875] [INFO] Task started: Prodigal
[2023-03-16 23:42:38,875] [INFO] Running command: cat /var/lib/cwl/stg87070755-84f7-44ca-ab07-4257383c2cdb/OceanDNA-a2510.fa | prodigal -d OceanDNA-a2510/cds.fna -a OceanDNA-a2510/protein.faa -g 11 -q > /dev/null
[2023-03-16 23:42:47,197] [INFO] Task succeeded: Prodigal
[2023-03-16 23:42:47,197] [INFO] Task started: HMMsearch
[2023-03-16 23:42:47,197] [INFO] Running command: hmmsearch --tblout OceanDNA-a2510/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg45edc875-1503-4f95-b98d-6be402b24843/dqc_reference/reference_markers.hmm OceanDNA-a2510/protein.faa > /dev/null
[2023-03-16 23:42:47,359] [INFO] Task succeeded: HMMsearch
[2023-03-16 23:42:47,360] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg87070755-84f7-44ca-ab07-4257383c2cdb/OceanDNA-a2510.fa]
[2023-03-16 23:42:47,371] [INFO] Query marker FASTA was written to OceanDNA-a2510/markers.fasta
[2023-03-16 23:42:47,372] [INFO] Task started: Blastn
[2023-03-16 23:42:47,373] [INFO] Running command: blastn -query OceanDNA-a2510/markers.fasta -db /var/lib/cwl/stg45edc875-1503-4f95-b98d-6be402b24843/dqc_reference/reference_markers.fasta -out OceanDNA-a2510/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:42:48,765] [INFO] Task succeeded: Blastn
[2023-03-16 23:42:48,766] [INFO] Selected 3 target genomes.
[2023-03-16 23:42:48,766] [INFO] Target genome list was writen to OceanDNA-a2510/target_genomes.txt
[2023-03-16 23:42:48,788] [INFO] Task started: fastANI
[2023-03-16 23:42:48,788] [INFO] Running command: fastANI --query /var/lib/cwl/stg87070755-84f7-44ca-ab07-4257383c2cdb/OceanDNA-a2510.fa --refList OceanDNA-a2510/target_genomes.txt --output OceanDNA-a2510/fastani_result.tsv --threads 1
[2023-03-16 23:42:50,408] [INFO] Task succeeded: fastANI
[2023-03-16 23:42:50,408] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg45edc875-1503-4f95-b98d-6be402b24843/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 23:42:50,408] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg45edc875-1503-4f95-b98d-6be402b24843/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 23:42:50,409] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 23:42:50,409] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 23:42:50,409] [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 23:42:50,409] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2510/tc_result.tsv
[2023-03-16 23:42:50,409] [INFO] ===== Taxonomy check completed =====
[2023-03-16 23:42:50,409] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 23:42:50,409] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg45edc875-1503-4f95-b98d-6be402b24843/dqc_reference/checkm_data
[2023-03-16 23:42:50,420] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 23:42:50,423] [INFO] Task started: CheckM
[2023-03-16 23:42:50,423] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2510/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2510/checkm_input OceanDNA-a2510/checkm_result
[2023-03-16 23:43:20,528] [INFO] Task succeeded: CheckM
[2023-03-16 23:43:20,529] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.30%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 23:43:20,531] [INFO] ===== Completeness check finished =====
[2023-03-16 23:43:20,531] [INFO] ===== Start GTDB Search =====
[2023-03-16 23:43:20,531] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2510/markers.fasta)
[2023-03-16 23:43:20,531] [INFO] Task started: Blastn
[2023-03-16 23:43:20,531] [INFO] Running command: blastn -query OceanDNA-a2510/markers.fasta -db /var/lib/cwl/stg45edc875-1503-4f95-b98d-6be402b24843/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2510/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:43:21,525] [INFO] Task succeeded: Blastn
[2023-03-16 23:43:21,526] [INFO] Selected 6 target genomes.
[2023-03-16 23:43:21,526] [INFO] Target genome list was writen to OceanDNA-a2510/target_genomes_gtdb.txt
[2023-03-16 23:43:21,557] [INFO] Task started: fastANI
[2023-03-16 23:43:21,557] [INFO] Running command: fastANI --query /var/lib/cwl/stg87070755-84f7-44ca-ab07-4257383c2cdb/OceanDNA-a2510.fa --refList OceanDNA-a2510/target_genomes_gtdb.txt --output OceanDNA-a2510/fastani_result_gtdb.tsv --threads 1
[2023-03-16 23:43:23,276] [INFO] Task succeeded: fastANI
[2023-03-16 23:43:23,280] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 23:43:23,280] [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_002495535.1	s__MGIIa-L1 sp002495535	99.4106	370	407	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002502605.1	s__MGIIa-L1 sp002502605	80.9023	213	407	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.35	99.06	0.87	0.87	3	-
GCA_013330285.1	s__MGIIa-L1 sp8160u	79.7011	141	407	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	97.88	96.83	0.79	0.69	4	-
GCA_009937025.1	s__MGIIa-L1 sp009937025	77.2857	64	407	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 23:43:23,280] [INFO] GTDB search result was written to OceanDNA-a2510/result_gtdb.tsv
[2023-03-16 23:43:23,280] [INFO] ===== GTDB Search completed =====
[2023-03-16 23:43:23,281] [INFO] DFAST_QC result json was written to OceanDNA-a2510/dqc_result.json
[2023-03-16 23:43:23,281] [INFO] DFAST_QC completed!
[2023-03-16 23:43:23,281] [INFO] Total running time: 0h0m47s