[2023-03-15 08:09:45,317] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:09:45,317] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:09:45,317] [INFO] DQC Reference Directory: /var/lib/cwl/stgf0472dd8-43ed-4a5d-8733-cd5dea998a0e/dqc_reference
[2023-03-15 08:09:46,523] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:09:46,523] [INFO] Task started: Prodigal
[2023-03-15 08:09:46,523] [INFO] Running command: cat /var/lib/cwl/stg0f1dbdf3-ced5-4f34-a6f4-5d8168e2b020/OceanDNA-b22722.fa | prodigal -d OceanDNA-b22722/cds.fna -a OceanDNA-b22722/protein.faa -g 11 -q > /dev/null
[2023-03-15 08:10:01,483] [INFO] Task succeeded: Prodigal
[2023-03-15 08:10:01,484] [INFO] Task started: HMMsearch
[2023-03-15 08:10:01,484] [INFO] Running command: hmmsearch --tblout OceanDNA-b22722/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf0472dd8-43ed-4a5d-8733-cd5dea998a0e/dqc_reference/reference_markers.hmm OceanDNA-b22722/protein.faa > /dev/null
[2023-03-15 08:10:01,795] [INFO] Task succeeded: HMMsearch
[2023-03-15 08:10:01,797] [INFO] Found 6/6 markers.
[2023-03-15 08:10:01,820] [INFO] Query marker FASTA was written to OceanDNA-b22722/markers.fasta
[2023-03-15 08:10:01,821] [INFO] Task started: Blastn
[2023-03-15 08:10:01,821] [INFO] Running command: blastn -query OceanDNA-b22722/markers.fasta -db /var/lib/cwl/stgf0472dd8-43ed-4a5d-8733-cd5dea998a0e/dqc_reference/reference_markers.fasta -out OceanDNA-b22722/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:10:02,410] [INFO] Task succeeded: Blastn
[2023-03-15 08:10:02,410] [INFO] Selected 6 target genomes.
[2023-03-15 08:10:02,411] [INFO] Target genome list was writen to OceanDNA-b22722/target_genomes.txt
[2023-03-15 08:10:02,415] [INFO] Task started: fastANI
[2023-03-15 08:10:02,415] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f1dbdf3-ced5-4f34-a6f4-5d8168e2b020/OceanDNA-b22722.fa --refList OceanDNA-b22722/target_genomes.txt --output OceanDNA-b22722/fastani_result.tsv --threads 1
[2023-03-15 08:10:06,112] [INFO] Task succeeded: fastANI
[2023-03-15 08:10:06,112] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf0472dd8-43ed-4a5d-8733-cd5dea998a0e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 08:10:06,113] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf0472dd8-43ed-4a5d-8733-cd5dea998a0e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 08:10:06,113] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 08:10:06,113] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 08:10:06,113] [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
--------------------------------------------------------------------------------
[2023-03-15 08:10:06,113] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22722/tc_result.tsv
[2023-03-15 08:10:06,113] [INFO] ===== Taxonomy check completed =====
[2023-03-15 08:10:06,113] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 08:10:06,113] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf0472dd8-43ed-4a5d-8733-cd5dea998a0e/dqc_reference/checkm_data
[2023-03-15 08:10:06,116] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 08:10:06,120] [INFO] Task started: CheckM
[2023-03-15 08:10:06,120] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22722/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22722/checkm_input OceanDNA-b22722/checkm_result
[2023-03-15 08:10:47,493] [INFO] Task succeeded: CheckM
[2023-03-15 08:10:47,493] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 08:10:47,499] [INFO] ===== Completeness check finished =====
[2023-03-15 08:10:47,499] [INFO] ===== Start GTDB Search =====
[2023-03-15 08:10:47,499] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22722/markers.fasta)
[2023-03-15 08:10:47,500] [INFO] Task started: Blastn
[2023-03-15 08:10:47,500] [INFO] Running command: blastn -query OceanDNA-b22722/markers.fasta -db /var/lib/cwl/stgf0472dd8-43ed-4a5d-8733-cd5dea998a0e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22722/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:10:48,217] [INFO] Task succeeded: Blastn
[2023-03-15 08:10:48,218] [INFO] Selected 8 target genomes.
[2023-03-15 08:10:48,218] [INFO] Target genome list was writen to OceanDNA-b22722/target_genomes_gtdb.txt
[2023-03-15 08:10:48,226] [INFO] Task started: fastANI
[2023-03-15 08:10:48,226] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f1dbdf3-ced5-4f34-a6f4-5d8168e2b020/OceanDNA-b22722.fa --refList OceanDNA-b22722/target_genomes_gtdb.txt --output OceanDNA-b22722/fastani_result_gtdb.tsv --threads 1
[2023-03-15 08:10:52,677] [INFO] Task succeeded: fastANI
[2023-03-15 08:10:52,682] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 08:10:52,682] [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_016776925.1	s__UBA1268 sp016776925	98.9355	702	802	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__UBA1268	95.0	98.79	96.90	0.88	0.85	13	conclusive
GCA_905477565.1	s__UBA1268 sp905477565	85.5422	325	802	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__UBA1268	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003509235.1	s__UBA1268 sp003509235	85.3088	474	802	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__UBA1268	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002694955.1	s__UBA1268 sp002694955	81.7701	280	802	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__UBA1268	95.0	98.59	98.49	0.92	0.91	3	-
GCA_018694455.1	s__UBA1268 sp018694455	79.8397	364	802	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__UBA1268	95.0	98.79	98.58	0.79	0.76	6	-
GCA_002862165.1	s__UBA1268 sp002862165	79.7815	292	802	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__UBA1268	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014238855.1	s__UBA1268 sp014238855	79.4576	417	802	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__UBA1268	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 08:10:52,682] [INFO] GTDB search result was written to OceanDNA-b22722/result_gtdb.tsv
[2023-03-15 08:10:52,682] [INFO] ===== GTDB Search completed =====
[2023-03-15 08:10:52,683] [INFO] DFAST_QC result json was written to OceanDNA-b22722/dqc_result.json
[2023-03-15 08:10:52,683] [INFO] DFAST_QC completed!
[2023-03-15 08:10:52,683] [INFO] Total running time: 0h1m7s