[2023-03-15 23:42:29,677] [INFO] DFAST_QC pipeline started.
[2023-03-15 23:42:29,677] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 23:42:29,677] [INFO] DQC Reference Directory: /var/lib/cwl/stg99dbbbfa-de08-4bdb-ad67-a87d4bf983c1/dqc_reference
[2023-03-15 23:42:31,280] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 23:42:31,280] [INFO] Task started: Prodigal
[2023-03-15 23:42:31,280] [INFO] Running command: cat /var/lib/cwl/stga0eb603f-744f-4f68-b12d-21e5cc67cc7f/OceanDNA-b4218.fa | prodigal -d OceanDNA-b4218/cds.fna -a OceanDNA-b4218/protein.faa -g 11 -q > /dev/null
[2023-03-15 23:42:51,738] [INFO] Task succeeded: Prodigal
[2023-03-15 23:42:51,739] [INFO] Task started: HMMsearch
[2023-03-15 23:42:51,739] [INFO] Running command: hmmsearch --tblout OceanDNA-b4218/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg99dbbbfa-de08-4bdb-ad67-a87d4bf983c1/dqc_reference/reference_markers.hmm OceanDNA-b4218/protein.faa > /dev/null
[2023-03-15 23:42:51,933] [INFO] Task succeeded: HMMsearch
[2023-03-15 23:42:51,933] [INFO] Found 6/6 markers.
[2023-03-15 23:42:51,951] [INFO] Query marker FASTA was written to OceanDNA-b4218/markers.fasta
[2023-03-15 23:42:51,952] [INFO] Task started: Blastn
[2023-03-15 23:42:51,952] [INFO] Running command: blastn -query OceanDNA-b4218/markers.fasta -db /var/lib/cwl/stg99dbbbfa-de08-4bdb-ad67-a87d4bf983c1/dqc_reference/reference_markers.fasta -out OceanDNA-b4218/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:42:52,468] [INFO] Task succeeded: Blastn
[2023-03-15 23:42:52,469] [INFO] Selected 25 target genomes.
[2023-03-15 23:42:52,469] [INFO] Target genome list was writen to OceanDNA-b4218/target_genomes.txt
[2023-03-15 23:42:52,485] [INFO] Task started: fastANI
[2023-03-15 23:42:52,485] [INFO] Running command: fastANI --query /var/lib/cwl/stga0eb603f-744f-4f68-b12d-21e5cc67cc7f/OceanDNA-b4218.fa --refList OceanDNA-b4218/target_genomes.txt --output OceanDNA-b4218/fastani_result.tsv --threads 1
[2023-03-15 23:43:11,869] [INFO] Task succeeded: fastANI
[2023-03-15 23:43:11,870] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg99dbbbfa-de08-4bdb-ad67-a87d4bf983c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 23:43:11,870] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg99dbbbfa-de08-4bdb-ad67-a87d4bf983c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 23:43:11,870] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 23:43:11,870] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 23:43:11,870] [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 23:43:11,871] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4218/tc_result.tsv
[2023-03-15 23:43:11,871] [INFO] ===== Taxonomy check completed =====
[2023-03-15 23:43:11,871] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 23:43:11,871] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg99dbbbfa-de08-4bdb-ad67-a87d4bf983c1/dqc_reference/checkm_data
[2023-03-15 23:43:11,873] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 23:43:11,905] [INFO] Task started: CheckM
[2023-03-15 23:43:11,905] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4218/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4218/checkm_input OceanDNA-b4218/checkm_result
[2023-03-15 23:44:05,669] [INFO] Task succeeded: CheckM
[2023-03-15 23:44:05,670] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 23:44:05,673] [INFO] ===== Completeness check finished =====
[2023-03-15 23:44:05,673] [INFO] ===== Start GTDB Search =====
[2023-03-15 23:44:05,673] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4218/markers.fasta)
[2023-03-15 23:44:05,673] [INFO] Task started: Blastn
[2023-03-15 23:44:05,673] [INFO] Running command: blastn -query OceanDNA-b4218/markers.fasta -db /var/lib/cwl/stg99dbbbfa-de08-4bdb-ad67-a87d4bf983c1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4218/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:44:06,393] [INFO] Task succeeded: Blastn
[2023-03-15 23:44:06,394] [INFO] Selected 8 target genomes.
[2023-03-15 23:44:06,394] [INFO] Target genome list was writen to OceanDNA-b4218/target_genomes_gtdb.txt
[2023-03-15 23:44:06,404] [INFO] Task started: fastANI
[2023-03-15 23:44:06,404] [INFO] Running command: fastANI --query /var/lib/cwl/stga0eb603f-744f-4f68-b12d-21e5cc67cc7f/OceanDNA-b4218.fa --refList OceanDNA-b4218/target_genomes_gtdb.txt --output OceanDNA-b4218/fastani_result_gtdb.tsv --threads 1
[2023-03-15 23:44:11,167] [INFO] Task succeeded: fastANI
[2023-03-15 23:44:11,172] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 23:44:11,172] [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_905479015.1	s__UBA4465 sp002470835	99.896	908	957	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__UBA4465	95.0	99.62	98.40	0.95	0.92	11	conclusive
GCA_905182375.1	s__UBA4465 sp905182375	94.178	762	957	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__UBA4465	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002292365.1	s__UBA4465 sp002292365	92.9026	731	957	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__UBA4465	95.0	99.58	99.58	0.82	0.82	2	-
GCA_905182655.1	s__UBA4465 sp905182655	89.4934	499	957	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__UBA4465	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002691385.1	s__UBA4465 sp002691385	83.9994	621	957	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__UBA4465	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902605755.1	s__UBA4465 sp902605755	80.2406	343	957	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__UBA4465	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013204595.1	s__UBA4465 sp013204595	77.9686	147	957	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__UBA4465	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 23:44:11,172] [INFO] GTDB search result was written to OceanDNA-b4218/result_gtdb.tsv
[2023-03-15 23:44:11,173] [INFO] ===== GTDB Search completed =====
[2023-03-15 23:44:11,173] [INFO] DFAST_QC result json was written to OceanDNA-b4218/dqc_result.json
[2023-03-15 23:44:11,173] [INFO] DFAST_QC completed!
[2023-03-15 23:44:11,173] [INFO] Total running time: 0h1m41s