[2023-03-14 12:49:51,289] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:49:51,292] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:49:51,292] [INFO] DQC Reference Directory: /var/lib/cwl/stg1ced0040-258a-4476-8d68-0637a91526b2/dqc_reference
[2023-03-14 12:49:52,738] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:49:52,738] [INFO] Task started: Prodigal
[2023-03-14 12:49:52,738] [INFO] Running command: cat /var/lib/cwl/stg5e1573dc-d9e4-4afa-9a05-ac1e594b6a25/OceanDNA-b45382.fa | prodigal -d OceanDNA-b45382/cds.fna -a OceanDNA-b45382/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:50:22,142] [INFO] Task succeeded: Prodigal
[2023-03-14 12:50:22,143] [INFO] Task started: HMMsearch
[2023-03-14 12:50:22,143] [INFO] Running command: hmmsearch --tblout OceanDNA-b45382/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1ced0040-258a-4476-8d68-0637a91526b2/dqc_reference/reference_markers.hmm OceanDNA-b45382/protein.faa > /dev/null
[2023-03-14 12:50:22,376] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:50:22,377] [INFO] Found 6/6 markers.
[2023-03-14 12:50:22,416] [INFO] Query marker FASTA was written to OceanDNA-b45382/markers.fasta
[2023-03-14 12:50:22,418] [INFO] Task started: Blastn
[2023-03-14 12:50:22,418] [INFO] Running command: blastn -query OceanDNA-b45382/markers.fasta -db /var/lib/cwl/stg1ced0040-258a-4476-8d68-0637a91526b2/dqc_reference/reference_markers.fasta -out OceanDNA-b45382/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:50:22,982] [INFO] Task succeeded: Blastn
[2023-03-14 12:50:22,986] [INFO] Selected 26 target genomes.
[2023-03-14 12:50:22,987] [INFO] Target genome list was writen to OceanDNA-b45382/target_genomes.txt
[2023-03-14 12:50:22,999] [INFO] Task started: fastANI
[2023-03-14 12:50:22,999] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e1573dc-d9e4-4afa-9a05-ac1e594b6a25/OceanDNA-b45382.fa --refList OceanDNA-b45382/target_genomes.txt --output OceanDNA-b45382/fastani_result.tsv --threads 1
[2023-03-14 12:50:45,064] [INFO] Task succeeded: fastANI
[2023-03-14 12:50:45,064] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1ced0040-258a-4476-8d68-0637a91526b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:50:45,064] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1ced0040-258a-4476-8d68-0637a91526b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:50:45,065] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:50:45,065] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 12:50:45,065] [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
--------------------------------------------------------------------------------
[2023-03-14 12:50:45,066] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45382/tc_result.tsv
[2023-03-14 12:50:45,068] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:50:45,068] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:50:45,068] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1ced0040-258a-4476-8d68-0637a91526b2/dqc_reference/checkm_data
[2023-03-14 12:50:45,071] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:50:45,079] [INFO] Task started: CheckM
[2023-03-14 12:50:45,079] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45382/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45382/checkm_input OceanDNA-b45382/checkm_result
[2023-03-14 12:51:52,901] [INFO] Task succeeded: CheckM
[2023-03-14 12:51:52,901] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.73%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 12:51:52,905] [INFO] ===== Completeness check finished =====
[2023-03-14 12:51:52,905] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:51:52,905] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45382/markers.fasta)
[2023-03-14 12:51:52,906] [INFO] Task started: Blastn
[2023-03-14 12:51:52,906] [INFO] Running command: blastn -query OceanDNA-b45382/markers.fasta -db /var/lib/cwl/stg1ced0040-258a-4476-8d68-0637a91526b2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45382/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:51:53,869] [INFO] Task succeeded: Blastn
[2023-03-14 12:51:53,877] [INFO] Selected 20 target genomes.
[2023-03-14 12:51:53,877] [INFO] Target genome list was writen to OceanDNA-b45382/target_genomes_gtdb.txt
[2023-03-14 12:51:53,890] [INFO] Task started: fastANI
[2023-03-14 12:51:53,890] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e1573dc-d9e4-4afa-9a05-ac1e594b6a25/OceanDNA-b45382.fa --refList OceanDNA-b45382/target_genomes_gtdb.txt --output OceanDNA-b45382/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:52:08,783] [INFO] Task succeeded: fastANI
[2023-03-14 12:52:08,787] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 12:52:08,787] [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_003245525.1	s__Lenti-02 sp003245525	78.6439	317	852	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__UBA1407;f__Lenti-02;g__Lenti-02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001603055.1	s__Lenti-02 sp001603055	78.4152	235	852	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__UBA1407;f__Lenti-02;g__Lenti-02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019136035.1	s__JAGVUW01 sp019136035	76.5706	54	852	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__UBA1407;f__Lenti-02;g__JAGVUW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903837355.1	s__CAILUI01 sp903837355	76.2517	88	852	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__UBA1407;f__Lenti-02;g__CAILUI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903834675.1	s__CAILUI01 sp903834675	75.9729	61	852	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__UBA1407;f__Lenti-02;g__CAILUI01	95.0	99.71	99.71	0.87	0.87	2	-
GCA_016935045.1	s__JAFGRS01 sp016935045	75.9584	61	852	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__UBA1407;f__Lenti-02;g__JAFGRS01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 12:52:08,788] [INFO] GTDB search result was written to OceanDNA-b45382/result_gtdb.tsv
[2023-03-14 12:52:08,788] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:52:08,788] [INFO] DFAST_QC result json was written to OceanDNA-b45382/dqc_result.json
[2023-03-14 12:52:08,789] [INFO] DFAST_QC completed!
[2023-03-14 12:52:08,789] [INFO] Total running time: 0h2m17s