[2023-03-18 10:54:49,213] [INFO] DFAST_QC pipeline started.
[2023-03-18 10:54:49,214] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 10:54:49,214] [INFO] DQC Reference Directory: /var/lib/cwl/stg1cd77633-aa51-4d33-a68f-878c8a075c2b/dqc_reference
[2023-03-18 10:54:50,356] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 10:54:50,356] [INFO] Task started: Prodigal
[2023-03-18 10:54:50,356] [INFO] Running command: cat /var/lib/cwl/stgccf3b0d8-11e4-407a-b1af-62eed2746b6b/OceanDNA-b4321.fa | prodigal -d OceanDNA-b4321/cds.fna -a OceanDNA-b4321/protein.faa -g 11 -q > /dev/null
[2023-03-18 10:54:58,025] [INFO] Task succeeded: Prodigal
[2023-03-18 10:54:58,026] [INFO] Task started: HMMsearch
[2023-03-18 10:54:58,026] [INFO] Running command: hmmsearch --tblout OceanDNA-b4321/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1cd77633-aa51-4d33-a68f-878c8a075c2b/dqc_reference/reference_markers.hmm OceanDNA-b4321/protein.faa > /dev/null
[2023-03-18 10:54:58,189] [INFO] Task succeeded: HMMsearch
[2023-03-18 10:54:58,190] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgccf3b0d8-11e4-407a-b1af-62eed2746b6b/OceanDNA-b4321.fa]
[2023-03-18 10:54:58,210] [INFO] Query marker FASTA was written to OceanDNA-b4321/markers.fasta
[2023-03-18 10:54:58,210] [INFO] Task started: Blastn
[2023-03-18 10:54:58,210] [INFO] Running command: blastn -query OceanDNA-b4321/markers.fasta -db /var/lib/cwl/stg1cd77633-aa51-4d33-a68f-878c8a075c2b/dqc_reference/reference_markers.fasta -out OceanDNA-b4321/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:54:58,701] [INFO] Task succeeded: Blastn
[2023-03-18 10:54:58,706] [INFO] Selected 20 target genomes.
[2023-03-18 10:54:58,706] [INFO] Target genome list was writen to OceanDNA-b4321/target_genomes.txt
[2023-03-18 10:54:58,718] [INFO] Task started: fastANI
[2023-03-18 10:54:58,719] [INFO] Running command: fastANI --query /var/lib/cwl/stgccf3b0d8-11e4-407a-b1af-62eed2746b6b/OceanDNA-b4321.fa --refList OceanDNA-b4321/target_genomes.txt --output OceanDNA-b4321/fastani_result.tsv --threads 1
[2023-03-18 10:55:09,606] [INFO] Task succeeded: fastANI
[2023-03-18 10:55:09,606] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1cd77633-aa51-4d33-a68f-878c8a075c2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 10:55:09,606] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1cd77633-aa51-4d33-a68f-878c8a075c2b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 10:55:09,607] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 10:55:09,607] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 10:55:09,607] [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 10:55:09,609] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4321/tc_result.tsv
[2023-03-18 10:55:09,613] [INFO] ===== Taxonomy check completed =====
[2023-03-18 10:55:09,613] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 10:55:09,613] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1cd77633-aa51-4d33-a68f-878c8a075c2b/dqc_reference/checkm_data
[2023-03-18 10:55:09,616] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 10:55:09,648] [INFO] Task started: CheckM
[2023-03-18 10:55:09,648] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4321/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4321/checkm_input OceanDNA-b4321/checkm_result
[2023-03-18 10:55:33,786] [INFO] Task succeeded: CheckM
[2023-03-18 10:55:33,786] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 10:55:33,790] [INFO] ===== Completeness check finished =====
[2023-03-18 10:55:33,790] [INFO] ===== Start GTDB Search =====
[2023-03-18 10:55:33,790] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4321/markers.fasta)
[2023-03-18 10:55:33,791] [INFO] Task started: Blastn
[2023-03-18 10:55:33,791] [INFO] Running command: blastn -query OceanDNA-b4321/markers.fasta -db /var/lib/cwl/stg1cd77633-aa51-4d33-a68f-878c8a075c2b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4321/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:55:34,454] [INFO] Task succeeded: Blastn
[2023-03-18 10:55:34,455] [INFO] Selected 16 target genomes.
[2023-03-18 10:55:34,455] [INFO] Target genome list was writen to OceanDNA-b4321/target_genomes_gtdb.txt
[2023-03-18 10:55:34,472] [INFO] Task started: fastANI
[2023-03-18 10:55:34,472] [INFO] Running command: fastANI --query /var/lib/cwl/stgccf3b0d8-11e4-407a-b1af-62eed2746b6b/OceanDNA-b4321.fa --refList OceanDNA-b4321/target_genomes_gtdb.txt --output OceanDNA-b4321/fastani_result_gtdb.tsv --threads 1
[2023-03-18 10:55:39,185] [INFO] Task succeeded: fastANI
[2023-03-18 10:55:39,191] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 10:55:39,191] [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_002696995.1	s__MED-G16 sp002696995	92.7862	292	427	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__MED-G16;g__MED-G16	95.0	95.99	95.99	0.74	0.74	2	-
GCA_002457315.1	s__MED-G16 sp002457315	84.216	293	427	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__MED-G16;g__MED-G16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902626505.1	s__MED-G16 sp902626505	79.516	201	427	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__MED-G16;g__MED-G16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002697405.1	s__MED-G16 sp002697405	79.4389	184	427	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__MED-G16;g__MED-G16	95.0	98.03	98.03	0.62	0.62	2	-
GCA_902634135.1	s__MED-G16 sp902634135	79.125	134	427	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__MED-G16;g__MED-G16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002701745.1	s__MED-G16 sp002701745	78.9472	156	427	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__MED-G16;g__MED-G16	95.0	96.78	96.78	0.79	0.79	2	-
GCA_002702205.1	s__MED-G16 sp002702205	77.9114	108	427	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__MED-G16;g__MED-G16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902523065.1	s__MED-G16 sp902523065	77.6182	130	427	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__MED-G16;g__MED-G16	95.0	96.84	95.61	0.92	0.88	9	-
GCA_902633975.1	s__MED-G16 sp902633975	77.1642	121	427	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__MED-G16;g__MED-G16	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 10:55:39,191] [INFO] GTDB search result was written to OceanDNA-b4321/result_gtdb.tsv
[2023-03-18 10:55:39,192] [INFO] ===== GTDB Search completed =====
[2023-03-18 10:55:39,193] [INFO] DFAST_QC result json was written to OceanDNA-b4321/dqc_result.json
[2023-03-18 10:55:39,193] [INFO] DFAST_QC completed!
[2023-03-18 10:55:39,193] [INFO] Total running time: 0h0m50s