[2023-03-16 14:50:25,003] [INFO] DFAST_QC pipeline started.
[2023-03-16 14:50:25,003] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 14:50:25,004] [INFO] DQC Reference Directory: /var/lib/cwl/stge47cfb46-007a-4eb5-8492-aa48aaf712a3/dqc_reference
[2023-03-16 14:50:26,398] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 14:50:26,398] [INFO] Task started: Prodigal
[2023-03-16 14:50:26,398] [INFO] Running command: cat /var/lib/cwl/stgcbdd539f-90d9-4e83-a863-99db592bdce8/OceanDNA-b17625.fa | prodigal -d OceanDNA-b17625/cds.fna -a OceanDNA-b17625/protein.faa -g 11 -q > /dev/null
[2023-03-16 14:50:57,723] [INFO] Task succeeded: Prodigal
[2023-03-16 14:50:57,723] [INFO] Task started: HMMsearch
[2023-03-16 14:50:57,723] [INFO] Running command: hmmsearch --tblout OceanDNA-b17625/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge47cfb46-007a-4eb5-8492-aa48aaf712a3/dqc_reference/reference_markers.hmm OceanDNA-b17625/protein.faa > /dev/null
[2023-03-16 14:50:57,970] [INFO] Task succeeded: HMMsearch
[2023-03-16 14:50:57,971] [INFO] Found 6/6 markers.
[2023-03-16 14:50:58,007] [INFO] Query marker FASTA was written to OceanDNA-b17625/markers.fasta
[2023-03-16 14:50:58,008] [INFO] Task started: Blastn
[2023-03-16 14:50:58,008] [INFO] Running command: blastn -query OceanDNA-b17625/markers.fasta -db /var/lib/cwl/stge47cfb46-007a-4eb5-8492-aa48aaf712a3/dqc_reference/reference_markers.fasta -out OceanDNA-b17625/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 14:50:58,711] [INFO] Task succeeded: Blastn
[2023-03-16 14:50:58,712] [INFO] Selected 25 target genomes.
[2023-03-16 14:50:58,712] [INFO] Target genome list was writen to OceanDNA-b17625/target_genomes.txt
[2023-03-16 14:50:58,723] [INFO] Task started: fastANI
[2023-03-16 14:50:58,723] [INFO] Running command: fastANI --query /var/lib/cwl/stgcbdd539f-90d9-4e83-a863-99db592bdce8/OceanDNA-b17625.fa --refList OceanDNA-b17625/target_genomes.txt --output OceanDNA-b17625/fastani_result.tsv --threads 1
[2023-03-16 14:51:26,883] [INFO] Task succeeded: fastANI
[2023-03-16 14:51:26,883] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge47cfb46-007a-4eb5-8492-aa48aaf712a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 14:51:26,884] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge47cfb46-007a-4eb5-8492-aa48aaf712a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 14:51:26,884] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 14:51:26,884] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 14:51:26,884] [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
--------------------------------------------------------------------------------
[2023-03-16 14:51:26,937] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17625/tc_result.tsv
[2023-03-16 14:51:26,937] [INFO] ===== Taxonomy check completed =====
[2023-03-16 14:51:26,938] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 14:51:26,938] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge47cfb46-007a-4eb5-8492-aa48aaf712a3/dqc_reference/checkm_data
[2023-03-16 14:51:26,941] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 14:51:26,978] [INFO] Task started: CheckM
[2023-03-16 14:51:26,978] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17625/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17625/checkm_input OceanDNA-b17625/checkm_result
[2023-03-16 14:52:42,989] [INFO] Task succeeded: CheckM
[2023-03-16 14:52:42,990] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 14:52:42,994] [INFO] ===== Completeness check finished =====
[2023-03-16 14:52:42,994] [INFO] ===== Start GTDB Search =====
[2023-03-16 14:52:42,994] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17625/markers.fasta)
[2023-03-16 14:52:42,995] [INFO] Task started: Blastn
[2023-03-16 14:52:42,995] [INFO] Running command: blastn -query OceanDNA-b17625/markers.fasta -db /var/lib/cwl/stge47cfb46-007a-4eb5-8492-aa48aaf712a3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17625/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 14:52:43,745] [INFO] Task succeeded: Blastn
[2023-03-16 14:52:43,746] [INFO] Selected 30 target genomes.
[2023-03-16 14:52:43,746] [INFO] Target genome list was writen to OceanDNA-b17625/target_genomes_gtdb.txt
[2023-03-16 14:52:45,088] [INFO] Task started: fastANI
[2023-03-16 14:52:45,088] [INFO] Running command: fastANI --query /var/lib/cwl/stgcbdd539f-90d9-4e83-a863-99db592bdce8/OceanDNA-b17625.fa --refList OceanDNA-b17625/target_genomes_gtdb.txt --output OceanDNA-b17625/fastani_result_gtdb.tsv --threads 1
[2023-03-16 14:53:03,640] [INFO] Task succeeded: fastANI
[2023-03-16 14:53:03,646] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 14:53:03,658] [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_018672475.1	s__GCA-2724215 sp018672475	76.2287	81	1486	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2724215	95.0	99.78	99.75	0.95	0.94	9	-
GCA_002724215.1	s__GCA-2724215 sp002724215	76.1891	144	1486	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2724215	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016187725.1	s__SICG01 sp016187725	75.9232	109	1486	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__SICG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009840005.1	s__GCA-2724215 sp009840005	75.8655	93	1486	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2724215	95.0	99.94	99.94	0.99	0.99	2	-
GCA_009691525.1	s__SICG01 sp009691525	75.8299	96	1486	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__SICG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009841115.1	s__GCA-2724215 sp009841115	75.749	82	1486	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2724215	95.0	99.89	99.89	0.98	0.96	3	-
GCA_016867395.1	s__SICG01 sp016867395	75.7048	98	1486	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__SICG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007571365.1	s__GCA-2724215 sp007571365	75.6549	89	1486	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2724215	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903893785.1	s__CAITNQ01 sp903893785	75.4475	59	1486	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__CAITNQ01	95.0	99.57	99.57	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-03-16 14:53:03,806] [INFO] GTDB search result was written to OceanDNA-b17625/result_gtdb.tsv
[2023-03-16 14:53:03,806] [INFO] ===== GTDB Search completed =====
[2023-03-16 14:53:03,807] [INFO] DFAST_QC result json was written to OceanDNA-b17625/dqc_result.json
[2023-03-16 14:53:03,807] [INFO] DFAST_QC completed!
[2023-03-16 14:53:03,807] [INFO] Total running time: 0h2m39s