[2023-03-17 11:08:00,413] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:08:00,413] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:08:00,413] [INFO] DQC Reference Directory: /var/lib/cwl/stgfe5af7de-b979-4ec3-aefa-3e61dcb4c79c/dqc_reference
[2023-03-17 11:08:01,530] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:08:01,530] [INFO] Task started: Prodigal
[2023-03-17 11:08:01,530] [INFO] Running command: cat /var/lib/cwl/stg0bf14d7b-7603-40db-9650-e4764130a68b/OceanDNA-b46617.fa | prodigal -d OceanDNA-b46617/cds.fna -a OceanDNA-b46617/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:08:27,819] [INFO] Task succeeded: Prodigal
[2023-03-17 11:08:27,819] [INFO] Task started: HMMsearch
[2023-03-17 11:08:27,819] [INFO] Running command: hmmsearch --tblout OceanDNA-b46617/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfe5af7de-b979-4ec3-aefa-3e61dcb4c79c/dqc_reference/reference_markers.hmm OceanDNA-b46617/protein.faa > /dev/null
[2023-03-17 11:08:28,006] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:08:28,007] [INFO] Found 6/6 markers.
[2023-03-17 11:08:28,026] [INFO] Query marker FASTA was written to OceanDNA-b46617/markers.fasta
[2023-03-17 11:08:28,028] [INFO] Task started: Blastn
[2023-03-17 11:08:28,028] [INFO] Running command: blastn -query OceanDNA-b46617/markers.fasta -db /var/lib/cwl/stgfe5af7de-b979-4ec3-aefa-3e61dcb4c79c/dqc_reference/reference_markers.fasta -out OceanDNA-b46617/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:08:28,563] [INFO] Task succeeded: Blastn
[2023-03-17 11:08:28,564] [INFO] Selected 20 target genomes.
[2023-03-17 11:08:28,564] [INFO] Target genome list was writen to OceanDNA-b46617/target_genomes.txt
[2023-03-17 11:08:28,577] [INFO] Task started: fastANI
[2023-03-17 11:08:28,577] [INFO] Running command: fastANI --query /var/lib/cwl/stg0bf14d7b-7603-40db-9650-e4764130a68b/OceanDNA-b46617.fa --refList OceanDNA-b46617/target_genomes.txt --output OceanDNA-b46617/fastani_result.tsv --threads 1
[2023-03-17 11:08:43,165] [INFO] Task succeeded: fastANI
[2023-03-17 11:08:43,166] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfe5af7de-b979-4ec3-aefa-3e61dcb4c79c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:08:43,166] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfe5af7de-b979-4ec3-aefa-3e61dcb4c79c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:08:43,166] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:08:43,166] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 11:08:43,166] [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
--------------------------------------------------------------------------------
[2023-03-17 11:08:43,167] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46617/tc_result.tsv
[2023-03-17 11:08:43,167] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:08:43,167] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:08:43,167] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfe5af7de-b979-4ec3-aefa-3e61dcb4c79c/dqc_reference/checkm_data
[2023-03-17 11:08:43,170] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:08:43,212] [INFO] Task started: CheckM
[2023-03-17 11:08:43,212] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46617/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46617/checkm_input OceanDNA-b46617/checkm_result
[2023-03-17 11:09:49,447] [INFO] Task succeeded: CheckM
[2023-03-17 11:09:49,448] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 11:09:49,450] [INFO] ===== Completeness check finished =====
[2023-03-17 11:09:49,451] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:09:49,451] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46617/markers.fasta)
[2023-03-17 11:09:49,452] [INFO] Task started: Blastn
[2023-03-17 11:09:49,452] [INFO] Running command: blastn -query OceanDNA-b46617/markers.fasta -db /var/lib/cwl/stgfe5af7de-b979-4ec3-aefa-3e61dcb4c79c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46617/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:09:50,235] [INFO] Task succeeded: Blastn
[2023-03-17 11:09:50,236] [INFO] Selected 14 target genomes.
[2023-03-17 11:09:50,237] [INFO] Target genome list was writen to OceanDNA-b46617/target_genomes_gtdb.txt
[2023-03-17 11:09:50,551] [INFO] Task started: fastANI
[2023-03-17 11:09:50,551] [INFO] Running command: fastANI --query /var/lib/cwl/stg0bf14d7b-7603-40db-9650-e4764130a68b/OceanDNA-b46617.fa --refList OceanDNA-b46617/target_genomes_gtdb.txt --output OceanDNA-b46617/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:09:58,089] [INFO] Task succeeded: fastANI
[2023-03-17 11:09:58,095] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 11:09:58,095] [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_002718935.1	s__UBA1100 sp002718935	97.8438	466	856	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1100;g__UBA1100	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002721895.1	s__UBA6614 sp002721895	82.2362	245	856	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1100;g__UBA6614	95.0	97.45	95.11	0.88	0.86	3	-
GCA_011523245.1	s__UBA1100 sp011523245	80.4185	201	856	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1100;g__UBA1100	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003517285.1	s__UBA1100 sp003517285	79.1304	196	856	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1100;g__UBA1100	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014382585.1	s__JACNJL01 sp014382585	77.861	299	856	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1100;g__JACNJL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015660155.1	s__JACNJL01 sp015660155	77.6205	156	856	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1100;g__JACNJL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014239365.1	s__JACNJL01 sp014239365	77.1569	257	856	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1100;g__JACNJL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014382705.1	s__UBA1096 sp014382705	76.3132	66	856	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 11:09:58,095] [INFO] GTDB search result was written to OceanDNA-b46617/result_gtdb.tsv
[2023-03-17 11:09:58,095] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:09:58,096] [INFO] DFAST_QC result json was written to OceanDNA-b46617/dqc_result.json
[2023-03-17 11:09:58,096] [INFO] DFAST_QC completed!
[2023-03-17 11:09:58,096] [INFO] Total running time: 0h1m58s