[2023-03-19 05:19:33,755] [INFO] DFAST_QC pipeline started.
[2023-03-19 05:19:33,755] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 05:19:33,755] [INFO] DQC Reference Directory: /var/lib/cwl/stg18b0d261-6951-4a87-838c-9edc7ff21975/dqc_reference
[2023-03-19 05:19:35,417] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 05:19:35,417] [INFO] Task started: Prodigal
[2023-03-19 05:19:35,417] [INFO] Running command: cat /var/lib/cwl/stgcb6580ea-3e51-41a9-b21f-a29dad1510dc/OceanDNA-a3054.fa | prodigal -d OceanDNA-a3054/cds.fna -a OceanDNA-a3054/protein.faa -g 11 -q > /dev/null
[2023-03-19 05:19:46,228] [INFO] Task succeeded: Prodigal
[2023-03-19 05:19:46,228] [INFO] Task started: HMMsearch
[2023-03-19 05:19:46,228] [INFO] Running command: hmmsearch --tblout OceanDNA-a3054/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg18b0d261-6951-4a87-838c-9edc7ff21975/dqc_reference/reference_markers.hmm OceanDNA-a3054/protein.faa > /dev/null
[2023-03-19 05:19:46,420] [INFO] Task succeeded: HMMsearch
[2023-03-19 05:19:46,421] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgcb6580ea-3e51-41a9-b21f-a29dad1510dc/OceanDNA-a3054.fa]
[2023-03-19 05:19:46,432] [INFO] Query marker FASTA was written to OceanDNA-a3054/markers.fasta
[2023-03-19 05:19:46,433] [INFO] Task started: Blastn
[2023-03-19 05:19:46,433] [INFO] Running command: blastn -query OceanDNA-a3054/markers.fasta -db /var/lib/cwl/stg18b0d261-6951-4a87-838c-9edc7ff21975/dqc_reference/reference_markers.fasta -out OceanDNA-a3054/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:19:46,862] [INFO] Task succeeded: Blastn
[2023-03-19 05:19:46,863] [INFO] Selected 5 target genomes.
[2023-03-19 05:19:46,863] [INFO] Target genome list was writen to OceanDNA-a3054/target_genomes.txt
[2023-03-19 05:19:46,866] [INFO] Task started: fastANI
[2023-03-19 05:19:46,866] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb6580ea-3e51-41a9-b21f-a29dad1510dc/OceanDNA-a3054.fa --refList OceanDNA-a3054/target_genomes.txt --output OceanDNA-a3054/fastani_result.tsv --threads 1
[2023-03-19 05:19:50,207] [INFO] Task succeeded: fastANI
[2023-03-19 05:19:50,207] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg18b0d261-6951-4a87-838c-9edc7ff21975/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 05:19:50,207] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg18b0d261-6951-4a87-838c-9edc7ff21975/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 05:19:50,208] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 05:19:50,208] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 05:19:50,208] [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
--------------------------------------------------------------------------------
[2023-03-19 05:19:50,208] [INFO] DFAST Taxonomy check result was written to OceanDNA-a3054/tc_result.tsv
[2023-03-19 05:19:50,208] [INFO] ===== Taxonomy check completed =====
[2023-03-19 05:19:50,208] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 05:19:50,208] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg18b0d261-6951-4a87-838c-9edc7ff21975/dqc_reference/checkm_data
[2023-03-19 05:19:50,211] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 05:19:50,216] [INFO] Task started: CheckM
[2023-03-19 05:19:50,216] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a3054/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a3054/checkm_input OceanDNA-a3054/checkm_result
[2023-03-19 05:20:24,070] [INFO] Task succeeded: CheckM
[2023-03-19 05:20:24,071] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.71%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 05:20:24,073] [INFO] ===== Completeness check finished =====
[2023-03-19 05:20:24,073] [INFO] ===== Start GTDB Search =====
[2023-03-19 05:20:24,073] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a3054/markers.fasta)
[2023-03-19 05:20:24,073] [INFO] Task started: Blastn
[2023-03-19 05:20:24,073] [INFO] Running command: blastn -query OceanDNA-a3054/markers.fasta -db /var/lib/cwl/stg18b0d261-6951-4a87-838c-9edc7ff21975/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a3054/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:20:24,474] [INFO] Task succeeded: Blastn
[2023-03-19 05:20:24,474] [INFO] Selected 9 target genomes.
[2023-03-19 05:20:24,474] [INFO] Target genome list was writen to OceanDNA-a3054/target_genomes_gtdb.txt
[2023-03-19 05:20:24,501] [INFO] Task started: fastANI
[2023-03-19 05:20:24,501] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb6580ea-3e51-41a9-b21f-a29dad1510dc/OceanDNA-a3054.fa --refList OceanDNA-a3054/target_genomes_gtdb.txt --output OceanDNA-a3054/fastani_result_gtdb.tsv --threads 1
[2023-03-19 05:20:27,466] [INFO] Task succeeded: fastANI
[2023-03-19 05:20:27,472] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 05:20:27,472] [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_002502295.1	s__Poseidonia sp002502295	99.6369	474	539	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002714305.1	s__Poseidonia sp002714305	80.6166	319	539	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	98.69	98.28	0.79	0.76	8	-
GCA_002704515.1	s__Poseidonia sp002704515	80.5795	309	539	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002725275.1	s__Poseidonia sp002725275	78.3347	188	539	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	96.76	96.60	0.76	0.75	3	-
GCA_002495645.1	s__Poseidonia sp002495645	78.1123	199	539	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	99.68	99.68	0.84	0.84	2	-
GCA_002722695.1	s__Poseidonia sp002722695	77.9159	171	539	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	99.22	99.22	0.79	0.79	3	-
GCA_902625885.1	s__Poseidonia sp902625885	77.8342	131	539	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016779705.1	s__Poseidonia sp016779705	77.2225	106	539	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 05:20:27,472] [INFO] GTDB search result was written to OceanDNA-a3054/result_gtdb.tsv
[2023-03-19 05:20:27,472] [INFO] ===== GTDB Search completed =====
[2023-03-19 05:20:27,473] [INFO] DFAST_QC result json was written to OceanDNA-a3054/dqc_result.json
[2023-03-19 05:20:27,473] [INFO] DFAST_QC completed!
[2023-03-19 05:20:27,473] [INFO] Total running time: 0h0m54s