[2023-03-17 09:05:02,543] [INFO] DFAST_QC pipeline started.
[2023-03-17 09:05:02,544] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 09:05:02,544] [INFO] DQC Reference Directory: /var/lib/cwl/stgeaca0633-a56d-433c-8c0a-de5c221420ac/dqc_reference
[2023-03-17 09:05:03,739] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 09:05:03,739] [INFO] Task started: Prodigal
[2023-03-17 09:05:03,739] [INFO] Running command: cat /var/lib/cwl/stgfdf64388-30ca-4428-ae20-c827cdd1aaba/OceanDNA-b45383.fa | prodigal -d OceanDNA-b45383/cds.fna -a OceanDNA-b45383/protein.faa -g 11 -q > /dev/null
[2023-03-17 09:06:36,845] [INFO] Task succeeded: Prodigal
[2023-03-17 09:06:36,845] [INFO] Task started: HMMsearch
[2023-03-17 09:06:36,845] [INFO] Running command: hmmsearch --tblout OceanDNA-b45383/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeaca0633-a56d-433c-8c0a-de5c221420ac/dqc_reference/reference_markers.hmm OceanDNA-b45383/protein.faa > /dev/null
[2023-03-17 09:06:37,279] [INFO] Task succeeded: HMMsearch
[2023-03-17 09:06:37,280] [INFO] Found 6/6 markers.
[2023-03-17 09:06:37,350] [INFO] Query marker FASTA was written to OceanDNA-b45383/markers.fasta
[2023-03-17 09:06:37,367] [INFO] Task started: Blastn
[2023-03-17 09:06:37,367] [INFO] Running command: blastn -query OceanDNA-b45383/markers.fasta -db /var/lib/cwl/stgeaca0633-a56d-433c-8c0a-de5c221420ac/dqc_reference/reference_markers.fasta -out OceanDNA-b45383/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:06:38,133] [INFO] Task succeeded: Blastn
[2023-03-17 09:06:38,134] [INFO] Selected 21 target genomes.
[2023-03-17 09:06:38,134] [INFO] Target genome list was writen to OceanDNA-b45383/target_genomes.txt
[2023-03-17 09:06:38,145] [INFO] Task started: fastANI
[2023-03-17 09:06:38,145] [INFO] Running command: fastANI --query /var/lib/cwl/stgfdf64388-30ca-4428-ae20-c827cdd1aaba/OceanDNA-b45383.fa --refList OceanDNA-b45383/target_genomes.txt --output OceanDNA-b45383/fastani_result.tsv --threads 1
[2023-03-17 09:06:53,048] [INFO] Task succeeded: fastANI
[2023-03-17 09:06:53,048] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeaca0633-a56d-433c-8c0a-de5c221420ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 09:06:53,048] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeaca0633-a56d-433c-8c0a-de5c221420ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 09:06:53,052] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 09:06:53,052] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 09:06:53,052] [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
Skermanella rosea	strain=KEMB 2255-458	GCA_016806835.2	1817965	1817965	type	True	74.5111	50	4185	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 09:06:53,052] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45383/tc_result.tsv
[2023-03-17 09:06:53,053] [INFO] ===== Taxonomy check completed =====
[2023-03-17 09:06:53,053] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 09:06:53,053] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeaca0633-a56d-433c-8c0a-de5c221420ac/dqc_reference/checkm_data
[2023-03-17 09:06:53,053] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 09:06:53,249] [INFO] Task started: CheckM
[2023-03-17 09:06:53,249] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45383/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45383/checkm_input OceanDNA-b45383/checkm_result
[2023-03-17 09:10:44,334] [INFO] Task succeeded: CheckM
[2023-03-17 09:10:44,334] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 3.70%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 09:10:44,365] [INFO] ===== Completeness check finished =====
[2023-03-17 09:10:44,365] [INFO] ===== Start GTDB Search =====
[2023-03-17 09:10:44,365] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45383/markers.fasta)
[2023-03-17 09:10:44,368] [INFO] Task started: Blastn
[2023-03-17 09:10:44,368] [INFO] Running command: blastn -query OceanDNA-b45383/markers.fasta -db /var/lib/cwl/stgeaca0633-a56d-433c-8c0a-de5c221420ac/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45383/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:10:45,643] [INFO] Task succeeded: Blastn
[2023-03-17 09:10:45,644] [INFO] Selected 29 target genomes.
[2023-03-17 09:10:45,644] [INFO] Target genome list was writen to OceanDNA-b45383/target_genomes_gtdb.txt
[2023-03-17 09:10:45,939] [INFO] Task started: fastANI
[2023-03-17 09:10:45,940] [INFO] Running command: fastANI --query /var/lib/cwl/stgfdf64388-30ca-4428-ae20-c827cdd1aaba/OceanDNA-b45383.fa --refList OceanDNA-b45383/target_genomes_gtdb.txt --output OceanDNA-b45383/fastani_result_gtdb.tsv --threads 1
[2023-03-17 09:11:08,582] [INFO] Task succeeded: fastANI
[2023-03-17 09:11:08,586] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 09:11:08,586] [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_018676675.1	s__JABHEG01 sp018676675	99.9616	3993	4185	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__UBA1407;f__JABHEG01;g__JABHEG01	95.0	99.97	99.96	0.96	0.95	4	conclusive
GCA_001803235.1	s__YB12-FULL-65-16 sp001803235	75.2523	128	4185	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__UBA1407;f__YB12-FULL-65-16;g__YB12-FULL-65-16	95.0	99.92	99.92	0.93	0.93	2	-
GCA_019136035.1	s__JAGVUW01 sp019136035	75.2484	65	4185	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__UBA1407;f__Lenti-02;g__JAGVUW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903834675.1	s__CAILUI01 sp903834675	75.1687	90	4185	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__UBA1407;f__Lenti-02;g__CAILUI01	95.0	99.71	99.71	0.87	0.87	2	-
GCA_903837355.1	s__CAILUI01 sp903837355	75.1669	110	4185	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__UBA1407;f__Lenti-02;g__CAILUI01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 09:11:08,587] [INFO] GTDB search result was written to OceanDNA-b45383/result_gtdb.tsv
[2023-03-17 09:11:08,587] [INFO] ===== GTDB Search completed =====
[2023-03-17 09:11:08,588] [INFO] DFAST_QC result json was written to OceanDNA-b45383/dqc_result.json
[2023-03-17 09:11:08,588] [INFO] DFAST_QC completed!
[2023-03-17 09:11:08,588] [INFO] Total running time: 0h6m6s