[2023-03-19 04:39:24,789] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:39:24,789] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:39:24,789] [INFO] DQC Reference Directory: /var/lib/cwl/stg619176bb-087a-4d8d-9a67-111cb38a49db/dqc_reference
[2023-03-19 04:39:26,517] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:39:26,518] [INFO] Task started: Prodigal
[2023-03-19 04:39:26,518] [INFO] Running command: cat /var/lib/cwl/stg301f316b-aacc-4285-98f3-cfb17cb94dc7/OceanDNA-b35836.fa | prodigal -d OceanDNA-b35836/cds.fna -a OceanDNA-b35836/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:39:35,430] [INFO] Task succeeded: Prodigal
[2023-03-19 04:39:35,430] [INFO] Task started: HMMsearch
[2023-03-19 04:39:35,431] [INFO] Running command: hmmsearch --tblout OceanDNA-b35836/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg619176bb-087a-4d8d-9a67-111cb38a49db/dqc_reference/reference_markers.hmm OceanDNA-b35836/protein.faa > /dev/null
[2023-03-19 04:39:35,679] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:39:35,680] [INFO] Found 6/6 markers.
[2023-03-19 04:39:35,694] [INFO] Query marker FASTA was written to OceanDNA-b35836/markers.fasta
[2023-03-19 04:39:35,695] [INFO] Task started: Blastn
[2023-03-19 04:39:35,695] [INFO] Running command: blastn -query OceanDNA-b35836/markers.fasta -db /var/lib/cwl/stg619176bb-087a-4d8d-9a67-111cb38a49db/dqc_reference/reference_markers.fasta -out OceanDNA-b35836/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:39:36,509] [INFO] Task succeeded: Blastn
[2023-03-19 04:39:36,509] [INFO] Selected 19 target genomes.
[2023-03-19 04:39:36,510] [INFO] Target genome list was writen to OceanDNA-b35836/target_genomes.txt
[2023-03-19 04:39:36,521] [INFO] Task started: fastANI
[2023-03-19 04:39:36,521] [INFO] Running command: fastANI --query /var/lib/cwl/stg301f316b-aacc-4285-98f3-cfb17cb94dc7/OceanDNA-b35836.fa --refList OceanDNA-b35836/target_genomes.txt --output OceanDNA-b35836/fastani_result.tsv --threads 1
[2023-03-19 04:39:45,039] [INFO] Task succeeded: fastANI
[2023-03-19 04:39:45,039] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg619176bb-087a-4d8d-9a67-111cb38a49db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:39:45,040] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg619176bb-087a-4d8d-9a67-111cb38a49db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:39:45,040] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:39:45,040] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 04:39:45,040] [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 04:39:45,040] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35836/tc_result.tsv
[2023-03-19 04:39:45,040] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:39:45,040] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:39:45,040] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg619176bb-087a-4d8d-9a67-111cb38a49db/dqc_reference/checkm_data
[2023-03-19 04:39:45,092] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:39:45,096] [INFO] Task started: CheckM
[2023-03-19 04:39:45,096] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35836/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35836/checkm_input OceanDNA-b35836/checkm_result
[2023-03-19 04:40:14,083] [INFO] Task succeeded: CheckM
[2023-03-19 04:40:14,084] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:40:14,086] [INFO] ===== Completeness check finished =====
[2023-03-19 04:40:14,086] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:40:14,086] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35836/markers.fasta)
[2023-03-19 04:40:14,088] [INFO] Task started: Blastn
[2023-03-19 04:40:14,088] [INFO] Running command: blastn -query OceanDNA-b35836/markers.fasta -db /var/lib/cwl/stg619176bb-087a-4d8d-9a67-111cb38a49db/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35836/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:40:15,287] [INFO] Task succeeded: Blastn
[2023-03-19 04:40:15,288] [INFO] Selected 18 target genomes.
[2023-03-19 04:40:15,288] [INFO] Target genome list was writen to OceanDNA-b35836/target_genomes_gtdb.txt
[2023-03-19 04:40:15,334] [INFO] Task started: fastANI
[2023-03-19 04:40:15,334] [INFO] Running command: fastANI --query /var/lib/cwl/stg301f316b-aacc-4285-98f3-cfb17cb94dc7/OceanDNA-b35836.fa --refList OceanDNA-b35836/target_genomes_gtdb.txt --output OceanDNA-b35836/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:40:22,499] [INFO] Task succeeded: fastANI
[2023-03-19 04:40:22,501] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 04:40:22,501] [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_018668255.1	s__UBA4457 sp018668255	99.7825	520	540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ga0077536;f__Ga0077536;g__UBA4457	95.0	99.79	99.69	0.94	0.91	8	conclusive
GCA_002390205.1	s__UBA4457 sp002390205	93.3094	419	540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ga0077536;f__Ga0077536;g__UBA4457	95.0	99.66	99.66	0.70	0.70	2	-
--------------------------------------------------------------------------------
[2023-03-19 04:40:22,502] [INFO] GTDB search result was written to OceanDNA-b35836/result_gtdb.tsv
[2023-03-19 04:40:22,502] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:40:22,502] [INFO] DFAST_QC result json was written to OceanDNA-b35836/dqc_result.json
[2023-03-19 04:40:22,502] [INFO] DFAST_QC completed!
[2023-03-19 04:40:22,502] [INFO] Total running time: 0h0m58s