[2023-03-19 03:50:07,851] [INFO] DFAST_QC pipeline started.
[2023-03-19 03:50:07,851] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 03:50:07,851] [INFO] DQC Reference Directory: /var/lib/cwl/stge52ecc18-17b7-4c14-9a46-b35163d8fa7d/dqc_reference
[2023-03-19 03:50:09,608] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 03:50:09,608] [INFO] Task started: Prodigal
[2023-03-19 03:50:09,608] [INFO] Running command: cat /var/lib/cwl/stg8349778e-bd1e-4021-9ddd-335272b59f7d/OceanDNA-b17217.fa | prodigal -d OceanDNA-b17217/cds.fna -a OceanDNA-b17217/protein.faa -g 11 -q > /dev/null
[2023-03-19 03:50:21,431] [INFO] Task succeeded: Prodigal
[2023-03-19 03:50:21,431] [INFO] Task started: HMMsearch
[2023-03-19 03:50:21,431] [INFO] Running command: hmmsearch --tblout OceanDNA-b17217/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge52ecc18-17b7-4c14-9a46-b35163d8fa7d/dqc_reference/reference_markers.hmm OceanDNA-b17217/protein.faa > /dev/null
[2023-03-19 03:50:21,661] [INFO] Task succeeded: HMMsearch
[2023-03-19 03:50:21,662] [INFO] Found 6/6 markers.
[2023-03-19 03:50:21,681] [INFO] Query marker FASTA was written to OceanDNA-b17217/markers.fasta
[2023-03-19 03:50:21,681] [INFO] Task started: Blastn
[2023-03-19 03:50:21,681] [INFO] Running command: blastn -query OceanDNA-b17217/markers.fasta -db /var/lib/cwl/stge52ecc18-17b7-4c14-9a46-b35163d8fa7d/dqc_reference/reference_markers.fasta -out OceanDNA-b17217/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:50:22,317] [INFO] Task succeeded: Blastn
[2023-03-19 03:50:22,318] [INFO] Selected 31 target genomes.
[2023-03-19 03:50:22,318] [INFO] Target genome list was writen to OceanDNA-b17217/target_genomes.txt
[2023-03-19 03:50:22,335] [INFO] Task started: fastANI
[2023-03-19 03:50:22,335] [INFO] Running command: fastANI --query /var/lib/cwl/stg8349778e-bd1e-4021-9ddd-335272b59f7d/OceanDNA-b17217.fa --refList OceanDNA-b17217/target_genomes.txt --output OceanDNA-b17217/fastani_result.tsv --threads 1
[2023-03-19 03:50:48,041] [INFO] Task succeeded: fastANI
[2023-03-19 03:50:48,041] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge52ecc18-17b7-4c14-9a46-b35163d8fa7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 03:50:48,042] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge52ecc18-17b7-4c14-9a46-b35163d8fa7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 03:50:48,042] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 03:50:48,042] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 03:50:48,042] [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
--------------------------------------------------------------------------------
[2023-03-19 03:50:48,042] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17217/tc_result.tsv
[2023-03-19 03:50:48,042] [INFO] ===== Taxonomy check completed =====
[2023-03-19 03:50:48,042] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 03:50:48,042] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge52ecc18-17b7-4c14-9a46-b35163d8fa7d/dqc_reference/checkm_data
[2023-03-19 03:50:48,045] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 03:50:48,049] [INFO] Task started: CheckM
[2023-03-19 03:50:48,049] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17217/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17217/checkm_input OceanDNA-b17217/checkm_result
[2023-03-19 03:51:21,566] [INFO] Task succeeded: CheckM
[2023-03-19 03:51:21,567] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.89%
Contamintation: 3.27%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 03:51:21,569] [INFO] ===== Completeness check finished =====
[2023-03-19 03:51:21,569] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:51:21,569] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17217/markers.fasta)
[2023-03-19 03:51:21,570] [INFO] Task started: Blastn
[2023-03-19 03:51:21,570] [INFO] Running command: blastn -query OceanDNA-b17217/markers.fasta -db /var/lib/cwl/stge52ecc18-17b7-4c14-9a46-b35163d8fa7d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17217/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:51:22,527] [INFO] Task succeeded: Blastn
[2023-03-19 03:51:22,528] [INFO] Selected 28 target genomes.
[2023-03-19 03:51:22,528] [INFO] Target genome list was writen to OceanDNA-b17217/target_genomes_gtdb.txt
[2023-03-19 03:51:22,574] [INFO] Task started: fastANI
[2023-03-19 03:51:22,575] [INFO] Running command: fastANI --query /var/lib/cwl/stg8349778e-bd1e-4021-9ddd-335272b59f7d/OceanDNA-b17217.fa --refList OceanDNA-b17217/target_genomes_gtdb.txt --output OceanDNA-b17217/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:51:36,370] [INFO] Task succeeded: fastANI
[2023-03-19 03:51:36,374] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 03:51:36,374] [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_009937285.1	s__UBA1138 sp009937285	78.4748	55	581	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA1138	95.0	99.12	98.44	0.93	0.79	16	-
GCA_015664885.1	s__UBA1138 sp003447875	76.8279	56	581	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA1138	95.0	99.72	99.64	0.94	0.92	3	-
GCA_002390225.1	s__UBA2589 sp002390225	76.737	95	581	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA2589	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002885.1	s__UBA2589 sp013002885	75.9578	66	581	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA2589	95.0	99.00	99.00	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2023-03-19 03:51:36,374] [INFO] GTDB search result was written to OceanDNA-b17217/result_gtdb.tsv
[2023-03-19 03:51:36,374] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:51:36,375] [INFO] DFAST_QC result json was written to OceanDNA-b17217/dqc_result.json
[2023-03-19 03:51:36,375] [INFO] DFAST_QC completed!
[2023-03-19 03:51:36,375] [INFO] Total running time: 0h1m29s