[2023-03-18 07:06:22,077] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:06:22,077] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:06:22,077] [INFO] DQC Reference Directory: /var/lib/cwl/stgb96e51fd-0fc1-4c85-9d38-a3ef66fd1786/dqc_reference
[2023-03-18 07:06:23,326] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:06:23,326] [INFO] Task started: Prodigal
[2023-03-18 07:06:23,326] [INFO] Running command: cat /var/lib/cwl/stg10d9feb0-13bb-4941-97de-dcc3ff7a4bc9/OceanDNA-b46636.fa | prodigal -d OceanDNA-b46636/cds.fna -a OceanDNA-b46636/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:06:42,594] [INFO] Task succeeded: Prodigal
[2023-03-18 07:06:42,594] [INFO] Task started: HMMsearch
[2023-03-18 07:06:42,594] [INFO] Running command: hmmsearch --tblout OceanDNA-b46636/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb96e51fd-0fc1-4c85-9d38-a3ef66fd1786/dqc_reference/reference_markers.hmm OceanDNA-b46636/protein.faa > /dev/null
[2023-03-18 07:06:42,785] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:06:42,785] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg10d9feb0-13bb-4941-97de-dcc3ff7a4bc9/OceanDNA-b46636.fa]
[2023-03-18 07:06:42,800] [INFO] Query marker FASTA was written to OceanDNA-b46636/markers.fasta
[2023-03-18 07:06:42,800] [INFO] Task started: Blastn
[2023-03-18 07:06:42,800] [INFO] Running command: blastn -query OceanDNA-b46636/markers.fasta -db /var/lib/cwl/stgb96e51fd-0fc1-4c85-9d38-a3ef66fd1786/dqc_reference/reference_markers.fasta -out OceanDNA-b46636/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:06:43,324] [INFO] Task succeeded: Blastn
[2023-03-18 07:06:43,325] [INFO] Selected 20 target genomes.
[2023-03-18 07:06:43,325] [INFO] Target genome list was writen to OceanDNA-b46636/target_genomes.txt
[2023-03-18 07:06:43,341] [INFO] Task started: fastANI
[2023-03-18 07:06:43,341] [INFO] Running command: fastANI --query /var/lib/cwl/stg10d9feb0-13bb-4941-97de-dcc3ff7a4bc9/OceanDNA-b46636.fa --refList OceanDNA-b46636/target_genomes.txt --output OceanDNA-b46636/fastani_result.tsv --threads 1
[2023-03-18 07:06:59,347] [INFO] Task succeeded: fastANI
[2023-03-18 07:06:59,348] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb96e51fd-0fc1-4c85-9d38-a3ef66fd1786/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:06:59,348] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb96e51fd-0fc1-4c85-9d38-a3ef66fd1786/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:06:59,348] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:06:59,348] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 07:06:59,348] [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 07:06:59,348] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46636/tc_result.tsv
[2023-03-18 07:06:59,348] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:06:59,348] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:06:59,349] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb96e51fd-0fc1-4c85-9d38-a3ef66fd1786/dqc_reference/checkm_data
[2023-03-18 07:06:59,351] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:06:59,354] [INFO] Task started: CheckM
[2023-03-18 07:06:59,355] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46636/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46636/checkm_input OceanDNA-b46636/checkm_result
[2023-03-18 07:07:50,022] [INFO] Task succeeded: CheckM
[2023-03-18 07:07:50,022] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 07:07:50,024] [INFO] ===== Completeness check finished =====
[2023-03-18 07:07:50,024] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:07:50,024] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46636/markers.fasta)
[2023-03-18 07:07:50,025] [INFO] Task started: Blastn
[2023-03-18 07:07:50,025] [INFO] Running command: blastn -query OceanDNA-b46636/markers.fasta -db /var/lib/cwl/stgb96e51fd-0fc1-4c85-9d38-a3ef66fd1786/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46636/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:07:50,736] [INFO] Task succeeded: Blastn
[2023-03-18 07:07:50,737] [INFO] Selected 18 target genomes.
[2023-03-18 07:07:50,737] [INFO] Target genome list was writen to OceanDNA-b46636/target_genomes_gtdb.txt
[2023-03-18 07:07:51,282] [INFO] Task started: fastANI
[2023-03-18 07:07:51,283] [INFO] Running command: fastANI --query /var/lib/cwl/stg10d9feb0-13bb-4941-97de-dcc3ff7a4bc9/OceanDNA-b46636.fa --refList OceanDNA-b46636/target_genomes_gtdb.txt --output OceanDNA-b46636/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:08:02,046] [INFO] Task succeeded: fastANI
[2023-03-18 07:08:02,050] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 07:08:02,050] [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_002721895.1	s__UBA6614 sp002721895	94.7557	567	619	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1100;g__UBA6614	95.0	97.45	95.11	0.88	0.86	3	-
GCA_002718935.1	s__UBA1100 sp002718935	79.5963	80	619	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1100;g__UBA1100	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002724615.1	s__UBA6614 sp002724615	78.0201	87	619	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1100;g__UBA6614	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014239365.1	s__JACNJL01 sp014239365	76.5866	71	619	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1100;g__JACNJL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005809105.1	s__SYLI01 sp005809105	75.5082	52	619	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1100;g__SYLI01	95.0	99.90	99.86	0.97	0.96	4	-
--------------------------------------------------------------------------------
[2023-03-18 07:08:02,050] [INFO] GTDB search result was written to OceanDNA-b46636/result_gtdb.tsv
[2023-03-18 07:08:02,050] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:08:02,051] [INFO] DFAST_QC result json was written to OceanDNA-b46636/dqc_result.json
[2023-03-18 07:08:02,051] [INFO] DFAST_QC completed!
[2023-03-18 07:08:02,051] [INFO] Total running time: 0h1m40s