[2023-03-16 07:07:05,927] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:07:05,928] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:07:05,928] [INFO] DQC Reference Directory: /var/lib/cwl/stg375cdf6d-5e4b-4b64-95c1-821d5ffb6daf/dqc_reference
[2023-03-16 07:07:07,043] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:07:07,043] [INFO] Task started: Prodigal
[2023-03-16 07:07:07,043] [INFO] Running command: cat /var/lib/cwl/stg330eeebe-5353-4ea9-a91e-8b33e1aef5a9/OceanDNA-b17136.fa | prodigal -d OceanDNA-b17136/cds.fna -a OceanDNA-b17136/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:07:22,387] [INFO] Task succeeded: Prodigal
[2023-03-16 07:07:22,387] [INFO] Task started: HMMsearch
[2023-03-16 07:07:22,387] [INFO] Running command: hmmsearch --tblout OceanDNA-b17136/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg375cdf6d-5e4b-4b64-95c1-821d5ffb6daf/dqc_reference/reference_markers.hmm OceanDNA-b17136/protein.faa > /dev/null
[2023-03-16 07:07:22,578] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:07:22,579] [INFO] Found 6/6 markers.
[2023-03-16 07:07:22,604] [INFO] Query marker FASTA was written to OceanDNA-b17136/markers.fasta
[2023-03-16 07:07:22,605] [INFO] Task started: Blastn
[2023-03-16 07:07:22,605] [INFO] Running command: blastn -query OceanDNA-b17136/markers.fasta -db /var/lib/cwl/stg375cdf6d-5e4b-4b64-95c1-821d5ffb6daf/dqc_reference/reference_markers.fasta -out OceanDNA-b17136/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:07:23,151] [INFO] Task succeeded: Blastn
[2023-03-16 07:07:23,152] [INFO] Selected 22 target genomes.
[2023-03-16 07:07:23,152] [INFO] Target genome list was writen to OceanDNA-b17136/target_genomes.txt
[2023-03-16 07:07:23,162] [INFO] Task started: fastANI
[2023-03-16 07:07:23,162] [INFO] Running command: fastANI --query /var/lib/cwl/stg330eeebe-5353-4ea9-a91e-8b33e1aef5a9/OceanDNA-b17136.fa --refList OceanDNA-b17136/target_genomes.txt --output OceanDNA-b17136/fastani_result.tsv --threads 1
[2023-03-16 07:07:37,590] [INFO] Task succeeded: fastANI
[2023-03-16 07:07:37,591] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg375cdf6d-5e4b-4b64-95c1-821d5ffb6daf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:07:37,591] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg375cdf6d-5e4b-4b64-95c1-821d5ffb6daf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:07:37,594] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 07:07:37,595] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 07:07:37,595] [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
Desulfomarina profundi	strain=KT2	GCA_019703855.1	2772557	2772557	type	True	75.851	57	795	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 07:07:37,595] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17136/tc_result.tsv
[2023-03-16 07:07:37,595] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:07:37,595] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:07:37,595] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg375cdf6d-5e4b-4b64-95c1-821d5ffb6daf/dqc_reference/checkm_data
[2023-03-16 07:07:37,596] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:07:37,622] [INFO] Task started: CheckM
[2023-03-16 07:07:37,622] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17136/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17136/checkm_input OceanDNA-b17136/checkm_result
[2023-03-16 07:08:19,079] [INFO] Task succeeded: CheckM
[2023-03-16 07:08:19,080] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.45%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 07:08:19,083] [INFO] ===== Completeness check finished =====
[2023-03-16 07:08:19,083] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:08:19,084] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17136/markers.fasta)
[2023-03-16 07:08:19,084] [INFO] Task started: Blastn
[2023-03-16 07:08:19,085] [INFO] Running command: blastn -query OceanDNA-b17136/markers.fasta -db /var/lib/cwl/stg375cdf6d-5e4b-4b64-95c1-821d5ffb6daf/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17136/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:08:19,963] [INFO] Task succeeded: Blastn
[2023-03-16 07:08:19,964] [INFO] Selected 22 target genomes.
[2023-03-16 07:08:19,964] [INFO] Target genome list was writen to OceanDNA-b17136/target_genomes_gtdb.txt
[2023-03-16 07:08:20,002] [INFO] Task started: fastANI
[2023-03-16 07:08:20,002] [INFO] Running command: fastANI --query /var/lib/cwl/stg330eeebe-5353-4ea9-a91e-8b33e1aef5a9/OceanDNA-b17136.fa --refList OceanDNA-b17136/target_genomes_gtdb.txt --output OceanDNA-b17136/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:08:33,028] [INFO] Task succeeded: fastANI
[2023-03-16 07:08:33,033] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 07:08:33,033] [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_013139415.1	s__Desulforhopalus sp013139415	80.2182	350	795	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulforhopalus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005116645.1	s__Desulforhopalus sp005116645	78.6274	296	795	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulforhopalus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000961725.1	s__Desulforhopalus sp000961725	76.6938	120	795	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulforhopalus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733995.1	s__Desulforhopalus sp002733995	76.62	54	795	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulforhopalus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011391225.1	s__Desulforhopalus sp011391225	76.5885	64	795	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulforhopalus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903875445.1	s__Desulforhopalus sp903875445	76.5138	96	795	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulforhopalus	95.0	99.93	99.88	0.93	0.87	5	-
--------------------------------------------------------------------------------
[2023-03-16 07:08:33,033] [INFO] GTDB search result was written to OceanDNA-b17136/result_gtdb.tsv
[2023-03-16 07:08:33,034] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:08:33,034] [INFO] DFAST_QC result json was written to OceanDNA-b17136/dqc_result.json
[2023-03-16 07:08:33,034] [INFO] DFAST_QC completed!
[2023-03-16 07:08:33,034] [INFO] Total running time: 0h1m27s