[2023-03-19 04:43:18,631] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:43:18,631] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:43:18,631] [INFO] DQC Reference Directory: /var/lib/cwl/stg1a82385c-d2f3-460c-b0b3-c512fb8fe01d/dqc_reference
[2023-03-19 04:43:19,743] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:43:19,743] [INFO] Task started: Prodigal
[2023-03-19 04:43:19,743] [INFO] Running command: cat /var/lib/cwl/stg87ab7fa5-89f5-442e-afbd-9bf95806ae17/OceanDNA-b44759.fa | prodigal -d OceanDNA-b44759/cds.fna -a OceanDNA-b44759/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:43:29,314] [INFO] Task succeeded: Prodigal
[2023-03-19 04:43:29,314] [INFO] Task started: HMMsearch
[2023-03-19 04:43:29,314] [INFO] Running command: hmmsearch --tblout OceanDNA-b44759/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1a82385c-d2f3-460c-b0b3-c512fb8fe01d/dqc_reference/reference_markers.hmm OceanDNA-b44759/protein.faa > /dev/null
[2023-03-19 04:43:29,472] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:43:29,473] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg87ab7fa5-89f5-442e-afbd-9bf95806ae17/OceanDNA-b44759.fa]
[2023-03-19 04:43:29,486] [INFO] Query marker FASTA was written to OceanDNA-b44759/markers.fasta
[2023-03-19 04:43:29,487] [INFO] Task started: Blastn
[2023-03-19 04:43:29,488] [INFO] Running command: blastn -query OceanDNA-b44759/markers.fasta -db /var/lib/cwl/stg1a82385c-d2f3-460c-b0b3-c512fb8fe01d/dqc_reference/reference_markers.fasta -out OceanDNA-b44759/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:43:30,032] [INFO] Task succeeded: Blastn
[2023-03-19 04:43:30,033] [INFO] Selected 8 target genomes.
[2023-03-19 04:43:30,033] [INFO] Target genome list was writen to OceanDNA-b44759/target_genomes.txt
[2023-03-19 04:43:30,038] [INFO] Task started: fastANI
[2023-03-19 04:43:30,038] [INFO] Running command: fastANI --query /var/lib/cwl/stg87ab7fa5-89f5-442e-afbd-9bf95806ae17/OceanDNA-b44759.fa --refList OceanDNA-b44759/target_genomes.txt --output OceanDNA-b44759/fastani_result.tsv --threads 1
[2023-03-19 04:43:35,102] [INFO] Task succeeded: fastANI
[2023-03-19 04:43:35,103] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1a82385c-d2f3-460c-b0b3-c512fb8fe01d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:43:35,103] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1a82385c-d2f3-460c-b0b3-c512fb8fe01d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:43:35,103] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:43:35,103] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 04:43:35,103] [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 04:43:35,103] [INFO] DFAST Taxonomy check result was written to OceanDNA-b44759/tc_result.tsv
[2023-03-19 04:43:35,103] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:43:35,104] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:43:35,104] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1a82385c-d2f3-460c-b0b3-c512fb8fe01d/dqc_reference/checkm_data
[2023-03-19 04:43:35,106] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:43:35,128] [INFO] Task started: CheckM
[2023-03-19 04:43:35,128] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b44759/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b44759/checkm_input OceanDNA-b44759/checkm_result
[2023-03-19 04:44:03,900] [INFO] Task succeeded: CheckM
[2023-03-19 04:44:03,901] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 04:44:03,903] [INFO] ===== Completeness check finished =====
[2023-03-19 04:44:03,903] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:44:03,903] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b44759/markers.fasta)
[2023-03-19 04:44:03,903] [INFO] Task started: Blastn
[2023-03-19 04:44:03,903] [INFO] Running command: blastn -query OceanDNA-b44759/markers.fasta -db /var/lib/cwl/stg1a82385c-d2f3-460c-b0b3-c512fb8fe01d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b44759/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:44:04,773] [INFO] Task succeeded: Blastn
[2023-03-19 04:44:04,774] [INFO] Selected 7 target genomes.
[2023-03-19 04:44:04,774] [INFO] Target genome list was writen to OceanDNA-b44759/target_genomes_gtdb.txt
[2023-03-19 04:44:04,783] [INFO] Task started: fastANI
[2023-03-19 04:44:04,783] [INFO] Running command: fastANI --query /var/lib/cwl/stg87ab7fa5-89f5-442e-afbd-9bf95806ae17/OceanDNA-b44759.fa --refList OceanDNA-b44759/target_genomes_gtdb.txt --output OceanDNA-b44759/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:44:08,801] [INFO] Task succeeded: fastANI
[2023-03-19 04:44:08,806] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 04:44:08,806] [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_018645085.1	s__Arctic96AD-7 sp018645085	88.2895	456	550	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002685535.1	s__Arctic96AD-7 sp002685535	87.7093	428	550	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	97.44	95.94	0.78	0.68	5	-
GCA_014381795.1	s__Arctic96AD-7 sp014381795	87.4106	336	550	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004213175.1	s__Arctic96AD-7 sp002704555	82.4685	332	550	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	97.39	96.63	0.73	0.69	4	-
GCA_016764995.1	s__Arctic96AD-7 sp016764995	81.0713	385	550	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012964265.1	s__Arctic96AD-7 sp012964265	79.9073	305	550	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	99.25	98.98	0.81	0.73	8	-
GCA_002082305.1	s__Arctic96AD-7 sp002082305	78.2485	241	550	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	98.68	95.22	0.86	0.64	13	-
--------------------------------------------------------------------------------
[2023-03-19 04:44:08,806] [INFO] GTDB search result was written to OceanDNA-b44759/result_gtdb.tsv
[2023-03-19 04:44:08,806] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:44:08,807] [INFO] DFAST_QC result json was written to OceanDNA-b44759/dqc_result.json
[2023-03-19 04:44:08,807] [INFO] DFAST_QC completed!
[2023-03-19 04:44:08,807] [INFO] Total running time: 0h0m50s