[2023-03-17 09:59:00,870] [INFO] DFAST_QC pipeline started.
[2023-03-17 09:59:00,877] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 09:59:00,877] [INFO] DQC Reference Directory: /var/lib/cwl/stgf986a4a4-9371-44ae-ba48-4ea17389469b/dqc_reference
[2023-03-17 09:59:02,026] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 09:59:02,027] [INFO] Task started: Prodigal
[2023-03-17 09:59:02,027] [INFO] Running command: cat /var/lib/cwl/stg87ac9023-08c3-4827-8cea-086735f896ac/OceanDNA-b41704.fa | prodigal -d OceanDNA-b41704/cds.fna -a OceanDNA-b41704/protein.faa -g 11 -q > /dev/null
[2023-03-17 09:59:06,677] [INFO] Task succeeded: Prodigal
[2023-03-17 09:59:06,677] [INFO] Task started: HMMsearch
[2023-03-17 09:59:06,677] [INFO] Running command: hmmsearch --tblout OceanDNA-b41704/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf986a4a4-9371-44ae-ba48-4ea17389469b/dqc_reference/reference_markers.hmm OceanDNA-b41704/protein.faa > /dev/null
[2023-03-17 09:59:06,894] [INFO] Task succeeded: HMMsearch
[2023-03-17 09:59:06,894] [INFO] Found 6/6 markers.
[2023-03-17 09:59:06,986] [INFO] Query marker FASTA was written to OceanDNA-b41704/markers.fasta
[2023-03-17 09:59:06,988] [INFO] Task started: Blastn
[2023-03-17 09:59:06,988] [INFO] Running command: blastn -query OceanDNA-b41704/markers.fasta -db /var/lib/cwl/stgf986a4a4-9371-44ae-ba48-4ea17389469b/dqc_reference/reference_markers.fasta -out OceanDNA-b41704/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:59:07,820] [INFO] Task succeeded: Blastn
[2023-03-17 09:59:07,829] [INFO] Selected 31 target genomes.
[2023-03-17 09:59:07,829] [INFO] Target genome list was writen to OceanDNA-b41704/target_genomes.txt
[2023-03-17 09:59:07,983] [INFO] Task started: fastANI
[2023-03-17 09:59:07,983] [INFO] Running command: fastANI --query /var/lib/cwl/stg87ac9023-08c3-4827-8cea-086735f896ac/OceanDNA-b41704.fa --refList OceanDNA-b41704/target_genomes.txt --output OceanDNA-b41704/fastani_result.tsv --threads 1
[2023-03-17 09:59:22,693] [INFO] Task succeeded: fastANI
[2023-03-17 09:59:22,694] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf986a4a4-9371-44ae-ba48-4ea17389469b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 09:59:22,694] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf986a4a4-9371-44ae-ba48-4ea17389469b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 09:59:22,694] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 09:59:22,694] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 09:59:22,694] [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
--------------------------------------------------------------------------------
[2023-03-17 09:59:22,700] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41704/tc_result.tsv
[2023-03-17 09:59:22,716] [INFO] ===== Taxonomy check completed =====
[2023-03-17 09:59:22,716] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 09:59:22,717] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf986a4a4-9371-44ae-ba48-4ea17389469b/dqc_reference/checkm_data
[2023-03-17 09:59:22,719] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 09:59:22,775] [INFO] Task started: CheckM
[2023-03-17 09:59:22,776] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41704/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41704/checkm_input OceanDNA-b41704/checkm_result
[2023-03-17 09:59:40,831] [INFO] Task succeeded: CheckM
[2023-03-17 09:59:40,831] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 09:59:41,077] [INFO] ===== Completeness check finished =====
[2023-03-17 09:59:41,077] [INFO] ===== Start GTDB Search =====
[2023-03-17 09:59:41,077] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41704/markers.fasta)
[2023-03-17 09:59:41,078] [INFO] Task started: Blastn
[2023-03-17 09:59:41,078] [INFO] Running command: blastn -query OceanDNA-b41704/markers.fasta -db /var/lib/cwl/stgf986a4a4-9371-44ae-ba48-4ea17389469b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41704/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:59:42,479] [INFO] Task succeeded: Blastn
[2023-03-17 09:59:42,494] [INFO] Selected 20 target genomes.
[2023-03-17 09:59:42,494] [INFO] Target genome list was writen to OceanDNA-b41704/target_genomes_gtdb.txt
[2023-03-17 09:59:43,057] [INFO] Task started: fastANI
[2023-03-17 09:59:43,057] [INFO] Running command: fastANI --query /var/lib/cwl/stg87ac9023-08c3-4827-8cea-086735f896ac/OceanDNA-b41704.fa --refList OceanDNA-b41704/target_genomes_gtdb.txt --output OceanDNA-b41704/fastani_result_gtdb.tsv --threads 1
[2023-03-17 09:59:48,003] [INFO] Task succeeded: fastANI
[2023-03-17 09:59:48,010] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 09:59:48,010] [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_003331625.1	s__MEDG-81 sp003331625	95.4759	252	294	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__MEDG-81	95.0	96.72	96.66	0.81	0.79	3	conclusive
GCA_902595715.1	s__MEDG-81 sp902595715	79.132	129	294	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__MEDG-81	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902632605.1	s__MEDG-81 sp902632605	78.7734	118	294	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__MEDG-81	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902625415.1	s__MEDG-81 sp902625415	78.7403	129	294	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__MEDG-81	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902561325.1	s__MEDG-81 sp902561325	78.7354	129	294	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__MEDG-81	95.0	98.13	98.13	0.81	0.81	2	-
GCA_003279605.1	s__MEDG-81 sp003279605	78.7323	152	294	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__MEDG-81	95.0	100.00	100.00	1.00	1.00	2	-
GCA_902629465.1	s__MEDG-81 sp902629465	78.6636	93	294	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__MEDG-81	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902514765.1	s__MEDG-81 sp902514765	78.642	111	294	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__MEDG-81	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902587545.1	s__MEDG-81 sp902587545	78.6254	141	294	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__MEDG-81	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003213595.1	s__MEDG-81 sp003213595	78.6202	135	294	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__MEDG-81	95.0	99.82	99.63	0.96	0.91	3	-
GCA_902540995.1	s__MEDG-81 sp902540995	78.4846	113	294	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__MEDG-81	95.0	98.42	98.42	0.80	0.80	2	-
--------------------------------------------------------------------------------
[2023-03-17 09:59:48,018] [INFO] GTDB search result was written to OceanDNA-b41704/result_gtdb.tsv
[2023-03-17 09:59:48,034] [INFO] ===== GTDB Search completed =====
[2023-03-17 09:59:48,046] [INFO] DFAST_QC result json was written to OceanDNA-b41704/dqc_result.json
[2023-03-17 09:59:48,047] [INFO] DFAST_QC completed!
[2023-03-17 09:59:48,047] [INFO] Total running time: 0h0m47s