[2023-03-18 01:59:39,784] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:59:39,786] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:59:39,786] [INFO] DQC Reference Directory: /var/lib/cwl/stgd40ce414-5622-4b5b-82f9-a6af9a4b8388/dqc_reference
[2023-03-18 01:59:40,956] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:59:40,956] [INFO] Task started: Prodigal
[2023-03-18 01:59:40,956] [INFO] Running command: cat /var/lib/cwl/stg0ca0e6d4-3778-48ce-b371-c3cac1c7e479/OceanDNA-b3419.fa | prodigal -d OceanDNA-b3419/cds.fna -a OceanDNA-b3419/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:59:47,452] [INFO] Task succeeded: Prodigal
[2023-03-18 01:59:47,453] [INFO] Task started: HMMsearch
[2023-03-18 01:59:47,453] [INFO] Running command: hmmsearch --tblout OceanDNA-b3419/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd40ce414-5622-4b5b-82f9-a6af9a4b8388/dqc_reference/reference_markers.hmm OceanDNA-b3419/protein.faa > /dev/null
[2023-03-18 01:59:47,609] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:59:47,610] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0ca0e6d4-3778-48ce-b371-c3cac1c7e479/OceanDNA-b3419.fa]
[2023-03-18 01:59:47,627] [INFO] Query marker FASTA was written to OceanDNA-b3419/markers.fasta
[2023-03-18 01:59:47,628] [INFO] Task started: Blastn
[2023-03-18 01:59:47,629] [INFO] Running command: blastn -query OceanDNA-b3419/markers.fasta -db /var/lib/cwl/stgd40ce414-5622-4b5b-82f9-a6af9a4b8388/dqc_reference/reference_markers.fasta -out OceanDNA-b3419/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:59:48,184] [INFO] Task succeeded: Blastn
[2023-03-18 01:59:48,194] [INFO] Selected 20 target genomes.
[2023-03-18 01:59:48,194] [INFO] Target genome list was writen to OceanDNA-b3419/target_genomes.txt
[2023-03-18 01:59:48,208] [INFO] Task started: fastANI
[2023-03-18 01:59:48,208] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ca0e6d4-3778-48ce-b371-c3cac1c7e479/OceanDNA-b3419.fa --refList OceanDNA-b3419/target_genomes.txt --output OceanDNA-b3419/fastani_result.tsv --threads 1
[2023-03-18 02:00:04,588] [INFO] Task succeeded: fastANI
[2023-03-18 02:00:04,589] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd40ce414-5622-4b5b-82f9-a6af9a4b8388/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:00:04,589] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd40ce414-5622-4b5b-82f9-a6af9a4b8388/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:00:04,589] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 02:00:04,589] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 02:00:04,590] [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
--------------------------------------------------------------------------------
[2023-03-18 02:00:04,592] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3419/tc_result.tsv
[2023-03-18 02:00:04,597] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:00:04,597] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:00:04,597] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd40ce414-5622-4b5b-82f9-a6af9a4b8388/dqc_reference/checkm_data
[2023-03-18 02:00:04,600] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:00:04,641] [INFO] Task started: CheckM
[2023-03-18 02:00:04,641] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3419/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3419/checkm_input OceanDNA-b3419/checkm_result
[2023-03-18 02:00:26,706] [INFO] Task succeeded: CheckM
[2023-03-18 02:00:26,707] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.93%
Contamintation: 3.47%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 02:00:26,774] [INFO] ===== Completeness check finished =====
[2023-03-18 02:00:26,774] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:00:26,775] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3419/markers.fasta)
[2023-03-18 02:00:26,776] [INFO] Task started: Blastn
[2023-03-18 02:00:26,776] [INFO] Running command: blastn -query OceanDNA-b3419/markers.fasta -db /var/lib/cwl/stgd40ce414-5622-4b5b-82f9-a6af9a4b8388/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3419/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:00:27,560] [INFO] Task succeeded: Blastn
[2023-03-18 02:00:27,564] [INFO] Selected 9 target genomes.
[2023-03-18 02:00:27,564] [INFO] Target genome list was writen to OceanDNA-b3419/target_genomes_gtdb.txt
[2023-03-18 02:00:27,598] [INFO] Task started: fastANI
[2023-03-18 02:00:27,598] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ca0e6d4-3778-48ce-b371-c3cac1c7e479/OceanDNA-b3419.fa --refList OceanDNA-b3419/target_genomes_gtdb.txt --output OceanDNA-b3419/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:00:31,851] [INFO] Task succeeded: fastANI
[2023-03-18 02:00:31,857] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 02:00:31,858] [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_016650125.1	s__67-14 sp016650125	79.3147	171	324	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__70-9;g__67-14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016712175.1	s__67-14 sp016712175	78.921	154	324	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__70-9;g__67-14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016649615.1	s__67-14 sp016649615	78.4245	113	324	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__70-9;g__67-14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017304845.1	s__67-14 sp017304845	78.2602	106	324	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__70-9;g__67-14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001897355.1	s__67-14 sp001897355	78.1481	151	324	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__70-9;g__67-14	95.0	99.98	99.98	0.99	0.99	2	-
GCA_903939845.1	s__67-14 sp903939845	76.8894	76	324	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__70-9;g__67-14	95.0	99.80	99.74	0.97	0.96	7	-
GCA_005885405.1	s__VAYN01 sp005885405	76.8751	58	324	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__70-9;g__VAYN01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 02:00:31,858] [INFO] GTDB search result was written to OceanDNA-b3419/result_gtdb.tsv
[2023-03-18 02:00:31,860] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:00:31,862] [INFO] DFAST_QC result json was written to OceanDNA-b3419/dqc_result.json
[2023-03-18 02:00:31,862] [INFO] DFAST_QC completed!
[2023-03-18 02:00:31,862] [INFO] Total running time: 0h0m52s