[2023-03-17 02:03:49,354] [INFO] DFAST_QC pipeline started.
[2023-03-17 02:03:49,354] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 02:03:49,354] [INFO] DQC Reference Directory: /var/lib/cwl/stge1a72ecd-e224-406b-a411-cdea994f6297/dqc_reference
[2023-03-17 02:03:50,601] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 02:03:50,601] [INFO] Task started: Prodigal
[2023-03-17 02:03:50,601] [INFO] Running command: cat /var/lib/cwl/stgaca5702d-2299-4e98-a30f-62eb211b7e30/OceanDNA-b1493.fa | prodigal -d OceanDNA-b1493/cds.fna -a OceanDNA-b1493/protein.faa -g 11 -q > /dev/null
[2023-03-17 02:04:06,393] [INFO] Task succeeded: Prodigal
[2023-03-17 02:04:06,393] [INFO] Task started: HMMsearch
[2023-03-17 02:04:06,393] [INFO] Running command: hmmsearch --tblout OceanDNA-b1493/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge1a72ecd-e224-406b-a411-cdea994f6297/dqc_reference/reference_markers.hmm OceanDNA-b1493/protein.faa > /dev/null
[2023-03-17 02:04:06,563] [INFO] Task succeeded: HMMsearch
[2023-03-17 02:04:06,564] [INFO] Found 6/6 markers.
[2023-03-17 02:04:06,581] [INFO] Query marker FASTA was written to OceanDNA-b1493/markers.fasta
[2023-03-17 02:04:06,582] [INFO] Task started: Blastn
[2023-03-17 02:04:06,582] [INFO] Running command: blastn -query OceanDNA-b1493/markers.fasta -db /var/lib/cwl/stge1a72ecd-e224-406b-a411-cdea994f6297/dqc_reference/reference_markers.fasta -out OceanDNA-b1493/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:04:07,091] [INFO] Task succeeded: Blastn
[2023-03-17 02:04:07,092] [INFO] Selected 20 target genomes.
[2023-03-17 02:04:07,092] [INFO] Target genome list was writen to OceanDNA-b1493/target_genomes.txt
[2023-03-17 02:04:07,102] [INFO] Task started: fastANI
[2023-03-17 02:04:07,102] [INFO] Running command: fastANI --query /var/lib/cwl/stgaca5702d-2299-4e98-a30f-62eb211b7e30/OceanDNA-b1493.fa --refList OceanDNA-b1493/target_genomes.txt --output OceanDNA-b1493/fastani_result.tsv --threads 1
[2023-03-17 02:04:16,645] [INFO] Task succeeded: fastANI
[2023-03-17 02:04:16,645] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge1a72ecd-e224-406b-a411-cdea994f6297/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 02:04:16,646] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge1a72ecd-e224-406b-a411-cdea994f6297/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 02:04:16,646] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 02:04:16,646] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 02:04:16,646] [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 02:04:16,646] [INFO] DFAST Taxonomy check result was written to OceanDNA-b1493/tc_result.tsv
[2023-03-17 02:04:16,646] [INFO] ===== Taxonomy check completed =====
[2023-03-17 02:04:16,646] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 02:04:16,646] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge1a72ecd-e224-406b-a411-cdea994f6297/dqc_reference/checkm_data
[2023-03-17 02:04:16,649] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 02:04:16,656] [INFO] Task started: CheckM
[2023-03-17 02:04:16,656] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b1493/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b1493/checkm_input OceanDNA-b1493/checkm_result
[2023-03-17 02:04:58,395] [INFO] Task succeeded: CheckM
[2023-03-17 02:04:58,395] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 02:04:58,398] [INFO] ===== Completeness check finished =====
[2023-03-17 02:04:58,398] [INFO] ===== Start GTDB Search =====
[2023-03-17 02:04:58,398] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b1493/markers.fasta)
[2023-03-17 02:04:58,398] [INFO] Task started: Blastn
[2023-03-17 02:04:58,398] [INFO] Running command: blastn -query OceanDNA-b1493/markers.fasta -db /var/lib/cwl/stge1a72ecd-e224-406b-a411-cdea994f6297/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b1493/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:04:59,104] [INFO] Task succeeded: Blastn
[2023-03-17 02:04:59,105] [INFO] Selected 11 target genomes.
[2023-03-17 02:04:59,105] [INFO] Target genome list was writen to OceanDNA-b1493/target_genomes_gtdb.txt
[2023-03-17 02:04:59,423] [INFO] Task started: fastANI
[2023-03-17 02:04:59,423] [INFO] Running command: fastANI --query /var/lib/cwl/stgaca5702d-2299-4e98-a30f-62eb211b7e30/OceanDNA-b1493.fa --refList OceanDNA-b1493/target_genomes_gtdb.txt --output OceanDNA-b1493/fastani_result_gtdb.tsv --threads 1
[2023-03-17 02:05:04,601] [INFO] Task succeeded: fastANI
[2023-03-17 02:05:04,606] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 02:05:04,606] [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_002331465.1	s__UBA2110 sp002331465	97.0098	609	860	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__UBA2110	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_012960315.1	s__UBA2110 sp012960315	94.123	791	860	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__UBA2110	95.0	99.85	99.85	0.95	0.95	2	-
GCA_014239555.1	s__UBA2110 sp014239555	90.3012	794	860	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__UBA2110	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002719335.1	s__UBA2110 sp002719335	84.5619	574	860	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__UBA2110	95.0	96.75	96.75	0.83	0.83	2	-
GCA_002388005.1	s__UBA2110 sp002388005	79.1782	399	860	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__UBA2110	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002705305.1	s__UBA2110 sp002705305	78.2692	358	860	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__UBA2110	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002457435.1	s__MedAcidi-G3 sp002457435	77.117	90	860	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__MedAcidi-G3	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 02:05:04,606] [INFO] GTDB search result was written to OceanDNA-b1493/result_gtdb.tsv
[2023-03-17 02:05:04,606] [INFO] ===== GTDB Search completed =====
[2023-03-17 02:05:04,607] [INFO] DFAST_QC result json was written to OceanDNA-b1493/dqc_result.json
[2023-03-17 02:05:04,607] [INFO] DFAST_QC completed!
[2023-03-17 02:05:04,607] [INFO] Total running time: 0h1m15s