[2023-03-16 17:38:34,147] [INFO] DFAST_QC pipeline started.
[2023-03-16 17:38:34,147] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 17:38:34,147] [INFO] DQC Reference Directory: /var/lib/cwl/stgd2ff6431-bcde-40ce-941f-de08f6211aa9/dqc_reference
[2023-03-16 17:38:35,422] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 17:38:35,422] [INFO] Task started: Prodigal
[2023-03-16 17:38:35,423] [INFO] Running command: cat /var/lib/cwl/stg33903943-a0da-40a3-9845-9a61a644083e/OceanDNA-b43530.fa | prodigal -d OceanDNA-b43530/cds.fna -a OceanDNA-b43530/protein.faa -g 11 -q > /dev/null
[2023-03-16 17:38:53,371] [INFO] Task succeeded: Prodigal
[2023-03-16 17:38:53,371] [INFO] Task started: HMMsearch
[2023-03-16 17:38:53,371] [INFO] Running command: hmmsearch --tblout OceanDNA-b43530/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd2ff6431-bcde-40ce-941f-de08f6211aa9/dqc_reference/reference_markers.hmm OceanDNA-b43530/protein.faa > /dev/null
[2023-03-16 17:38:53,570] [INFO] Task succeeded: HMMsearch
[2023-03-16 17:38:53,571] [INFO] Found 6/6 markers.
[2023-03-16 17:38:53,592] [INFO] Query marker FASTA was written to OceanDNA-b43530/markers.fasta
[2023-03-16 17:38:53,593] [INFO] Task started: Blastn
[2023-03-16 17:38:53,593] [INFO] Running command: blastn -query OceanDNA-b43530/markers.fasta -db /var/lib/cwl/stgd2ff6431-bcde-40ce-941f-de08f6211aa9/dqc_reference/reference_markers.fasta -out OceanDNA-b43530/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:38:54,173] [INFO] Task succeeded: Blastn
[2023-03-16 17:38:54,175] [INFO] Selected 20 target genomes.
[2023-03-16 17:38:54,175] [INFO] Target genome list was writen to OceanDNA-b43530/target_genomes.txt
[2023-03-16 17:38:54,184] [INFO] Task started: fastANI
[2023-03-16 17:38:54,185] [INFO] Running command: fastANI --query /var/lib/cwl/stg33903943-a0da-40a3-9845-9a61a644083e/OceanDNA-b43530.fa --refList OceanDNA-b43530/target_genomes.txt --output OceanDNA-b43530/fastani_result.tsv --threads 1
[2023-03-16 17:39:05,539] [INFO] Task succeeded: fastANI
[2023-03-16 17:39:05,539] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd2ff6431-bcde-40ce-941f-de08f6211aa9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 17:39:05,539] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd2ff6431-bcde-40ce-941f-de08f6211aa9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 17:39:05,539] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 17:39:05,539] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 17:39:05,539] [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
--------------------------------------------------------------------------------
[2023-03-16 17:39:05,540] [INFO] DFAST Taxonomy check result was written to OceanDNA-b43530/tc_result.tsv
[2023-03-16 17:39:05,541] [INFO] ===== Taxonomy check completed =====
[2023-03-16 17:39:05,541] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 17:39:05,541] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd2ff6431-bcde-40ce-941f-de08f6211aa9/dqc_reference/checkm_data
[2023-03-16 17:39:05,544] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 17:39:05,591] [INFO] Task started: CheckM
[2023-03-16 17:39:05,591] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b43530/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b43530/checkm_input OceanDNA-b43530/checkm_result
[2023-03-16 17:40:05,861] [INFO] Task succeeded: CheckM
[2023-03-16 17:40:05,862] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 17:40:05,882] [INFO] ===== Completeness check finished =====
[2023-03-16 17:40:05,883] [INFO] ===== Start GTDB Search =====
[2023-03-16 17:40:05,883] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b43530/markers.fasta)
[2023-03-16 17:40:05,884] [INFO] Task started: Blastn
[2023-03-16 17:40:05,884] [INFO] Running command: blastn -query OceanDNA-b43530/markers.fasta -db /var/lib/cwl/stgd2ff6431-bcde-40ce-941f-de08f6211aa9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b43530/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:40:07,220] [INFO] Task succeeded: Blastn
[2023-03-16 17:40:07,223] [INFO] Selected 12 target genomes.
[2023-03-16 17:40:07,223] [INFO] Target genome list was writen to OceanDNA-b43530/target_genomes_gtdb.txt
[2023-03-16 17:40:07,268] [INFO] Task started: fastANI
[2023-03-16 17:40:07,268] [INFO] Running command: fastANI --query /var/lib/cwl/stg33903943-a0da-40a3-9845-9a61a644083e/OceanDNA-b43530.fa --refList OceanDNA-b43530/target_genomes_gtdb.txt --output OceanDNA-b43530/fastani_result_gtdb.tsv --threads 1
[2023-03-16 17:40:13,978] [INFO] Task succeeded: fastANI
[2023-03-16 17:40:13,982] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 17:40:13,982] [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_002731295.1	s__REDSEA-S09-B13 sp002731295	94.2536	639	994	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__REDSEA-S09-B13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002456995.1	s__REDSEA-S09-B13 sp002456995	91.6462	453	994	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__REDSEA-S09-B13	95.0	96.76	96.75	0.88	0.88	3	-
GCA_001629395.1	s__REDSEA-S09-B13 sp001629395	91.6319	673	994	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__REDSEA-S09-B13	95.0	98.93	98.69	0.85	0.83	6	-
GCA_003447825.1	s__REDSEA-S09-B13 sp003447825	87.8134	787	994	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__REDSEA-S09-B13	95.0	99.33	99.08	0.90	0.86	16	-
GCA_002718155.1	s__UBA9619 sp002718155	77.8922	93	994	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Arenicellales;f__UBA868;g__UBA9619	95.0	99.32	99.28	0.82	0.80	3	-
--------------------------------------------------------------------------------
[2023-03-16 17:40:13,983] [INFO] GTDB search result was written to OceanDNA-b43530/result_gtdb.tsv
[2023-03-16 17:40:13,983] [INFO] ===== GTDB Search completed =====
[2023-03-16 17:40:13,984] [INFO] DFAST_QC result json was written to OceanDNA-b43530/dqc_result.json
[2023-03-16 17:40:13,985] [INFO] DFAST_QC completed!
[2023-03-16 17:40:13,985] [INFO] Total running time: 0h1m40s