[2023-03-18 01:54:19,369] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:54:19,370] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:54:19,370] [INFO] DQC Reference Directory: /var/lib/cwl/stge1517234-527e-4121-a030-71cbe6f0a638/dqc_reference
[2023-03-18 01:54:20,447] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:54:20,448] [INFO] Task started: Prodigal
[2023-03-18 01:54:20,448] [INFO] Running command: cat /var/lib/cwl/stg82f10858-d1f1-4cbc-9440-64d3d28f0c69/OceanDNA-b46741.fa | prodigal -d OceanDNA-b46741/cds.fna -a OceanDNA-b46741/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:54:46,244] [INFO] Task succeeded: Prodigal
[2023-03-18 01:54:46,244] [INFO] Task started: HMMsearch
[2023-03-18 01:54:46,244] [INFO] Running command: hmmsearch --tblout OceanDNA-b46741/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge1517234-527e-4121-a030-71cbe6f0a638/dqc_reference/reference_markers.hmm OceanDNA-b46741/protein.faa > /dev/null
[2023-03-18 01:54:46,448] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:54:46,448] [INFO] Found 6/6 markers.
[2023-03-18 01:54:46,469] [INFO] Query marker FASTA was written to OceanDNA-b46741/markers.fasta
[2023-03-18 01:54:46,470] [INFO] Task started: Blastn
[2023-03-18 01:54:46,470] [INFO] Running command: blastn -query OceanDNA-b46741/markers.fasta -db /var/lib/cwl/stge1517234-527e-4121-a030-71cbe6f0a638/dqc_reference/reference_markers.fasta -out OceanDNA-b46741/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:54:46,975] [INFO] Task succeeded: Blastn
[2023-03-18 01:54:46,976] [INFO] Selected 15 target genomes.
[2023-03-18 01:54:46,976] [INFO] Target genome list was writen to OceanDNA-b46741/target_genomes.txt
[2023-03-18 01:54:46,985] [INFO] Task started: fastANI
[2023-03-18 01:54:46,985] [INFO] Running command: fastANI --query /var/lib/cwl/stg82f10858-d1f1-4cbc-9440-64d3d28f0c69/OceanDNA-b46741.fa --refList OceanDNA-b46741/target_genomes.txt --output OceanDNA-b46741/fastani_result.tsv --threads 1
[2023-03-18 01:54:59,928] [INFO] Task succeeded: fastANI
[2023-03-18 01:54:59,929] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge1517234-527e-4121-a030-71cbe6f0a638/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:54:59,929] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge1517234-527e-4121-a030-71cbe6f0a638/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:54:59,929] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:54:59,929] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 01:54:59,929] [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 01:54:59,929] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46741/tc_result.tsv
[2023-03-18 01:54:59,929] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:54:59,930] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:54:59,930] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge1517234-527e-4121-a030-71cbe6f0a638/dqc_reference/checkm_data
[2023-03-18 01:54:59,932] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:54:59,946] [INFO] Task started: CheckM
[2023-03-18 01:54:59,946] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46741/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46741/checkm_input OceanDNA-b46741/checkm_result
[2023-03-18 01:56:06,410] [INFO] Task succeeded: CheckM
[2023-03-18 01:56:06,410] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 1.39%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 01:56:06,454] [INFO] ===== Completeness check finished =====
[2023-03-18 01:56:06,454] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:56:06,455] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46741/markers.fasta)
[2023-03-18 01:56:06,456] [INFO] Task started: Blastn
[2023-03-18 01:56:06,456] [INFO] Running command: blastn -query OceanDNA-b46741/markers.fasta -db /var/lib/cwl/stge1517234-527e-4121-a030-71cbe6f0a638/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46741/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:56:07,161] [INFO] Task succeeded: Blastn
[2023-03-18 01:56:07,162] [INFO] Selected 15 target genomes.
[2023-03-18 01:56:07,162] [INFO] Target genome list was writen to OceanDNA-b46741/target_genomes_gtdb.txt
[2023-03-18 01:56:07,174] [INFO] Task started: fastANI
[2023-03-18 01:56:07,174] [INFO] Running command: fastANI --query /var/lib/cwl/stg82f10858-d1f1-4cbc-9440-64d3d28f0c69/OceanDNA-b46741.fa --refList OceanDNA-b46741/target_genomes_gtdb.txt --output OceanDNA-b46741/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:56:17,466] [INFO] Task succeeded: fastANI
[2023-03-18 01:56:17,472] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 01:56:17,472] [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_002723015.1	s__Roseibacillus_B sp002723015	99.3406	978	1032	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	99.32	99.32	0.93	0.93	2	conclusive
GCA_002686085.1	s__Roseibacillus_B sp002686085	79.4139	565	1032	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	99.30	99.30	0.96	0.96	3	-
GCA_002420305.1	s__Roseibacillus_B sp002420305	79.3216	550	1032	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	97.44	96.53	0.87	0.86	5	-
GCA_002380675.1	s__Roseibacillus_B sp002380675	79.2108	458	1032	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	99.08	99.08	0.81	0.81	2	-
GCA_002709915.1	s__Roseibacillus_B sp002709915	79.017	415	1032	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	99.45	99.45	0.86	0.86	2	-
GCA_002729275.1	s__Roseibacillus_B sp002729275	78.8297	523	1032	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	98.94	98.88	0.91	0.89	3	-
GCA_002715825.1	s__Roseibacillus_B sp002715825	78.6549	453	1032	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	99.08	98.76	0.87	0.85	4	-
GCA_002721695.1	s__Roseibacillus_B sp002721695	77.4413	167	1032	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 01:56:17,472] [INFO] GTDB search result was written to OceanDNA-b46741/result_gtdb.tsv
[2023-03-18 01:56:17,472] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:56:17,473] [INFO] DFAST_QC result json was written to OceanDNA-b46741/dqc_result.json
[2023-03-18 01:56:17,473] [INFO] DFAST_QC completed!
[2023-03-18 01:56:17,473] [INFO] Total running time: 0h1m58s