[2023-03-15 12:44:24,472] [INFO] DFAST_QC pipeline started.
[2023-03-15 12:44:24,472] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 12:44:24,472] [INFO] DQC Reference Directory: /var/lib/cwl/stg137aa4d4-88f7-4cbe-b2cc-9f4ea1b9c3cb/dqc_reference
[2023-03-15 12:44:26,207] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 12:44:26,208] [INFO] Task started: Prodigal
[2023-03-15 12:44:26,208] [INFO] Running command: cat /var/lib/cwl/stg00c6e76a-efd4-44d9-a320-b52b0bf55fac/OceanDNA-b4297.fa | prodigal -d OceanDNA-b4297/cds.fna -a OceanDNA-b4297/protein.faa -g 11 -q > /dev/null
[2023-03-15 12:44:33,262] [INFO] Task succeeded: Prodigal
[2023-03-15 12:44:33,263] [INFO] Task started: HMMsearch
[2023-03-15 12:44:33,263] [INFO] Running command: hmmsearch --tblout OceanDNA-b4297/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg137aa4d4-88f7-4cbe-b2cc-9f4ea1b9c3cb/dqc_reference/reference_markers.hmm OceanDNA-b4297/protein.faa > /dev/null
[2023-03-15 12:44:33,448] [INFO] Task succeeded: HMMsearch
[2023-03-15 12:44:33,448] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg00c6e76a-efd4-44d9-a320-b52b0bf55fac/OceanDNA-b4297.fa]
[2023-03-15 12:44:33,459] [INFO] Query marker FASTA was written to OceanDNA-b4297/markers.fasta
[2023-03-15 12:44:33,459] [INFO] Task started: Blastn
[2023-03-15 12:44:33,459] [INFO] Running command: blastn -query OceanDNA-b4297/markers.fasta -db /var/lib/cwl/stg137aa4d4-88f7-4cbe-b2cc-9f4ea1b9c3cb/dqc_reference/reference_markers.fasta -out OceanDNA-b4297/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:44:33,978] [INFO] Task succeeded: Blastn
[2023-03-15 12:44:33,979] [INFO] Selected 17 target genomes.
[2023-03-15 12:44:33,979] [INFO] Target genome list was writen to OceanDNA-b4297/target_genomes.txt
[2023-03-15 12:44:33,990] [INFO] Task started: fastANI
[2023-03-15 12:44:33,990] [INFO] Running command: fastANI --query /var/lib/cwl/stg00c6e76a-efd4-44d9-a320-b52b0bf55fac/OceanDNA-b4297.fa --refList OceanDNA-b4297/target_genomes.txt --output OceanDNA-b4297/fastani_result.tsv --threads 1
[2023-03-15 12:44:43,700] [INFO] Task succeeded: fastANI
[2023-03-15 12:44:43,701] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg137aa4d4-88f7-4cbe-b2cc-9f4ea1b9c3cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 12:44:43,701] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg137aa4d4-88f7-4cbe-b2cc-9f4ea1b9c3cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 12:44:43,701] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 12:44:43,701] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 12:44:43,701] [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
--------------------------------------------------------------------------------
[2023-03-15 12:44:43,702] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4297/tc_result.tsv
[2023-03-15 12:44:43,702] [INFO] ===== Taxonomy check completed =====
[2023-03-15 12:44:43,702] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 12:44:43,702] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg137aa4d4-88f7-4cbe-b2cc-9f4ea1b9c3cb/dqc_reference/checkm_data
[2023-03-15 12:44:43,705] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 12:44:43,708] [INFO] Task started: CheckM
[2023-03-15 12:44:43,708] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4297/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4297/checkm_input OceanDNA-b4297/checkm_result
[2023-03-15 12:45:06,594] [INFO] Task succeeded: CheckM
[2023-03-15 12:45:06,594] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 12:45:06,596] [INFO] ===== Completeness check finished =====
[2023-03-15 12:45:06,596] [INFO] ===== Start GTDB Search =====
[2023-03-15 12:45:06,596] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4297/markers.fasta)
[2023-03-15 12:45:06,596] [INFO] Task started: Blastn
[2023-03-15 12:45:06,596] [INFO] Running command: blastn -query OceanDNA-b4297/markers.fasta -db /var/lib/cwl/stg137aa4d4-88f7-4cbe-b2cc-9f4ea1b9c3cb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4297/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:45:07,336] [INFO] Task succeeded: Blastn
[2023-03-15 12:45:07,337] [INFO] Selected 24 target genomes.
[2023-03-15 12:45:07,337] [INFO] Target genome list was writen to OceanDNA-b4297/target_genomes_gtdb.txt
[2023-03-15 12:45:07,477] [INFO] Task started: fastANI
[2023-03-15 12:45:07,477] [INFO] Running command: fastANI --query /var/lib/cwl/stg00c6e76a-efd4-44d9-a320-b52b0bf55fac/OceanDNA-b4297.fa --refList OceanDNA-b4297/target_genomes_gtdb.txt --output OceanDNA-b4297/fastani_result_gtdb.tsv --threads 1
[2023-03-15 12:45:15,330] [INFO] Task succeeded: fastANI
[2023-03-15 12:45:15,334] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 12:45:15,335] [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_902529805.1	s__GCA-2715645 sp902529805	93.6043	333	387	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__MED-G16;g__GCA-2715645	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902628365.1	s__GCA-2715645 sp902628365	87.6679	252	387	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__MED-G16;g__GCA-2715645	95.0	97.14	96.28	0.66	0.65	3	-
GCA_902626505.1	s__MED-G16 sp902626505	77.4101	94	387	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	76.949	67	387	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	76.3769	55	387	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	76.3395	65	387	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	-
--------------------------------------------------------------------------------
[2023-03-15 12:45:15,335] [INFO] GTDB search result was written to OceanDNA-b4297/result_gtdb.tsv
[2023-03-15 12:45:15,335] [INFO] ===== GTDB Search completed =====
[2023-03-15 12:45:15,336] [INFO] DFAST_QC result json was written to OceanDNA-b4297/dqc_result.json
[2023-03-15 12:45:15,336] [INFO] DFAST_QC completed!
[2023-03-15 12:45:15,336] [INFO] Total running time: 0h0m51s