[2023-03-17 03:03:53,447] [INFO] DFAST_QC pipeline started.
[2023-03-17 03:03:53,447] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 03:03:53,447] [INFO] DQC Reference Directory: /var/lib/cwl/stgefadd291-5f23-4402-ac17-d049d6654df1/dqc_reference
[2023-03-17 03:03:54,540] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 03:03:54,541] [INFO] Task started: Prodigal
[2023-03-17 03:03:54,541] [INFO] Running command: cat /var/lib/cwl/stgfa0359c6-d305-4ab4-8318-84976ffdac43/OceanDNA-b45747.fa | prodigal -d OceanDNA-b45747/cds.fna -a OceanDNA-b45747/protein.faa -g 11 -q > /dev/null
[2023-03-17 03:04:25,948] [INFO] Task succeeded: Prodigal
[2023-03-17 03:04:25,948] [INFO] Task started: HMMsearch
[2023-03-17 03:04:25,949] [INFO] Running command: hmmsearch --tblout OceanDNA-b45747/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgefadd291-5f23-4402-ac17-d049d6654df1/dqc_reference/reference_markers.hmm OceanDNA-b45747/protein.faa > /dev/null
[2023-03-17 03:04:26,161] [INFO] Task succeeded: HMMsearch
[2023-03-17 03:04:26,162] [INFO] Found 6/6 markers.
[2023-03-17 03:04:26,185] [INFO] Query marker FASTA was written to OceanDNA-b45747/markers.fasta
[2023-03-17 03:04:26,186] [INFO] Task started: Blastn
[2023-03-17 03:04:26,186] [INFO] Running command: blastn -query OceanDNA-b45747/markers.fasta -db /var/lib/cwl/stgefadd291-5f23-4402-ac17-d049d6654df1/dqc_reference/reference_markers.fasta -out OceanDNA-b45747/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:04:26,761] [INFO] Task succeeded: Blastn
[2023-03-17 03:04:26,761] [INFO] Selected 14 target genomes.
[2023-03-17 03:04:26,762] [INFO] Target genome list was writen to OceanDNA-b45747/target_genomes.txt
[2023-03-17 03:04:26,858] [INFO] Task started: fastANI
[2023-03-17 03:04:26,858] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa0359c6-d305-4ab4-8318-84976ffdac43/OceanDNA-b45747.fa --refList OceanDNA-b45747/target_genomes.txt --output OceanDNA-b45747/fastani_result.tsv --threads 1
[2023-03-17 03:04:34,608] [INFO] Task succeeded: fastANI
[2023-03-17 03:04:34,608] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgefadd291-5f23-4402-ac17-d049d6654df1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 03:04:34,608] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgefadd291-5f23-4402-ac17-d049d6654df1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 03:04:34,608] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 03:04:34,609] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 03:04:34,609] [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 03:04:34,609] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45747/tc_result.tsv
[2023-03-17 03:04:34,609] [INFO] ===== Taxonomy check completed =====
[2023-03-17 03:04:34,609] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 03:04:34,609] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgefadd291-5f23-4402-ac17-d049d6654df1/dqc_reference/checkm_data
[2023-03-17 03:04:34,612] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 03:04:34,618] [INFO] Task started: CheckM
[2023-03-17 03:04:34,618] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45747/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45747/checkm_input OceanDNA-b45747/checkm_result
[2023-03-17 03:05:52,202] [INFO] Task succeeded: CheckM
[2023-03-17 03:05:52,202] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 03:05:52,206] [INFO] ===== Completeness check finished =====
[2023-03-17 03:05:52,206] [INFO] ===== Start GTDB Search =====
[2023-03-17 03:05:52,206] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45747/markers.fasta)
[2023-03-17 03:05:52,207] [INFO] Task started: Blastn
[2023-03-17 03:05:52,207] [INFO] Running command: blastn -query OceanDNA-b45747/markers.fasta -db /var/lib/cwl/stgefadd291-5f23-4402-ac17-d049d6654df1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45747/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:05:53,178] [INFO] Task succeeded: Blastn
[2023-03-17 03:05:53,179] [INFO] Selected 23 target genomes.
[2023-03-17 03:05:53,179] [INFO] Target genome list was writen to OceanDNA-b45747/target_genomes_gtdb.txt
[2023-03-17 03:05:53,271] [INFO] Task started: fastANI
[2023-03-17 03:05:53,271] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa0359c6-d305-4ab4-8318-84976ffdac43/OceanDNA-b45747.fa --refList OceanDNA-b45747/target_genomes_gtdb.txt --output OceanDNA-b45747/fastani_result_gtdb.tsv --threads 1
[2023-03-17 03:06:05,354] [INFO] Task succeeded: fastANI
[2023-03-17 03:06:05,358] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 03:06:05,358] [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_002500665.1	s__MB11C04 sp002500665	99.7787	1124	1198	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	98.37	95.55	0.93	0.84	7	conclusive
GCA_018695085.1	s__GCA-2730975 sp018695085	79.2196	113	1198	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__GCA-2730975	95.0	98.14	98.04	0.72	0.68	4	-
GCA_018645725.1	s__MB11C04 sp018645725	78.7891	358	1198	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002722545.1	s__MB11C04 sp002722545	77.5773	167	1198	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 03:06:05,358] [INFO] GTDB search result was written to OceanDNA-b45747/result_gtdb.tsv
[2023-03-17 03:06:05,358] [INFO] ===== GTDB Search completed =====
[2023-03-17 03:06:05,359] [INFO] DFAST_QC result json was written to OceanDNA-b45747/dqc_result.json
[2023-03-17 03:06:05,359] [INFO] DFAST_QC completed!
[2023-03-17 03:06:05,359] [INFO] Total running time: 0h2m12s