[2023-03-18 23:44:06,361] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:44:06,361] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:44:06,361] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ef69118-6489-41f3-ba74-cfa5414ae389/dqc_reference
[2023-03-18 23:44:07,497] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:44:07,497] [INFO] Task started: Prodigal
[2023-03-18 23:44:07,498] [INFO] Running command: cat /var/lib/cwl/stg55c1c17e-9f6d-426a-b093-65dbfec82bb8/OceanDNA-b21144.fa | prodigal -d OceanDNA-b21144/cds.fna -a OceanDNA-b21144/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:44:14,286] [INFO] Task succeeded: Prodigal
[2023-03-18 23:44:14,287] [INFO] Task started: HMMsearch
[2023-03-18 23:44:14,287] [INFO] Running command: hmmsearch --tblout OceanDNA-b21144/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ef69118-6489-41f3-ba74-cfa5414ae389/dqc_reference/reference_markers.hmm OceanDNA-b21144/protein.faa > /dev/null
[2023-03-18 23:44:14,485] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:44:14,485] [INFO] Found 6/6 markers.
[2023-03-18 23:44:14,498] [INFO] Query marker FASTA was written to OceanDNA-b21144/markers.fasta
[2023-03-18 23:44:14,499] [INFO] Task started: Blastn
[2023-03-18 23:44:14,499] [INFO] Running command: blastn -query OceanDNA-b21144/markers.fasta -db /var/lib/cwl/stg8ef69118-6489-41f3-ba74-cfa5414ae389/dqc_reference/reference_markers.fasta -out OceanDNA-b21144/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:44:15,052] [INFO] Task succeeded: Blastn
[2023-03-18 23:44:15,053] [INFO] Selected 24 target genomes.
[2023-03-18 23:44:15,053] [INFO] Target genome list was writen to OceanDNA-b21144/target_genomes.txt
[2023-03-18 23:44:15,072] [INFO] Task started: fastANI
[2023-03-18 23:44:15,072] [INFO] Running command: fastANI --query /var/lib/cwl/stg55c1c17e-9f6d-426a-b093-65dbfec82bb8/OceanDNA-b21144.fa --refList OceanDNA-b21144/target_genomes.txt --output OceanDNA-b21144/fastani_result.tsv --threads 1
[2023-03-18 23:44:27,677] [INFO] Task succeeded: fastANI
[2023-03-18 23:44:27,677] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8ef69118-6489-41f3-ba74-cfa5414ae389/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:44:27,677] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8ef69118-6489-41f3-ba74-cfa5414ae389/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:44:27,678] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:44:27,678] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 23:44:27,678] [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
--------------------------------------------------------------------------------
[2023-03-18 23:44:27,678] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21144/tc_result.tsv
[2023-03-18 23:44:27,678] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:44:27,678] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:44:27,678] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ef69118-6489-41f3-ba74-cfa5414ae389/dqc_reference/checkm_data
[2023-03-18 23:44:27,681] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:44:27,786] [INFO] Task started: CheckM
[2023-03-18 23:44:27,787] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21144/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21144/checkm_input OceanDNA-b21144/checkm_result
[2023-03-18 23:44:50,580] [INFO] Task succeeded: CheckM
[2023-03-18 23:44:50,581] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.89%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:44:50,586] [INFO] ===== Completeness check finished =====
[2023-03-18 23:44:50,586] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:44:50,586] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21144/markers.fasta)
[2023-03-18 23:44:50,587] [INFO] Task started: Blastn
[2023-03-18 23:44:50,587] [INFO] Running command: blastn -query OceanDNA-b21144/markers.fasta -db /var/lib/cwl/stg8ef69118-6489-41f3-ba74-cfa5414ae389/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21144/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:44:51,497] [INFO] Task succeeded: Blastn
[2023-03-18 23:44:51,500] [INFO] Selected 14 target genomes.
[2023-03-18 23:44:51,500] [INFO] Target genome list was writen to OceanDNA-b21144/target_genomes_gtdb.txt
[2023-03-18 23:44:51,513] [INFO] Task started: fastANI
[2023-03-18 23:44:51,513] [INFO] Running command: fastANI --query /var/lib/cwl/stg55c1c17e-9f6d-426a-b093-65dbfec82bb8/OceanDNA-b21144.fa --refList OceanDNA-b21144/target_genomes_gtdb.txt --output OceanDNA-b21144/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:44:57,140] [INFO] Task succeeded: fastANI
[2023-03-18 23:44:57,148] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 23:44:57,149] [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_002705185.1	s__LS-NOB sp002705185	85.191	288	392	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014382285.1	s__LS-NOB sp014382285	79.2703	263	392	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	99.85	99.85	0.92	0.92	2	-
GCA_905612265.1	s__LS-NOB sp905612265	78.0136	85	392	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001542995.1	s__LS-NOB sp001542995	77.6152	175	392	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002786505.1	s__LS-NOB sp002786505	77.2732	144	392	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018673915.1	s__LS-NOB sp018673915	76.9012	98	392	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	99.92	99.88	0.94	0.90	12	-
GCA_003545625.1	s__LS-NOB sp003545625	76.848	76	392	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	98.65	98.65	0.77	0.77	2	-
GCA_018653085.1	s__LS-NOB sp018653085	76.4706	120	392	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	99.81	99.70	0.96	0.92	14	-
GCA_018664975.1	s__LS-NOB sp018664975	76.4314	74	392	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:44:57,150] [INFO] GTDB search result was written to OceanDNA-b21144/result_gtdb.tsv
[2023-03-18 23:44:57,150] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:44:57,153] [INFO] DFAST_QC result json was written to OceanDNA-b21144/dqc_result.json
[2023-03-18 23:44:57,153] [INFO] DFAST_QC completed!
[2023-03-18 23:44:57,153] [INFO] Total running time: 0h0m51s