[2023-03-17 06:30:49,799] [INFO] DFAST_QC pipeline started.
[2023-03-17 06:30:49,800] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 06:30:49,800] [INFO] DQC Reference Directory: /var/lib/cwl/stg911efb5c-c7ce-4354-a4ca-3df2be41ba6a/dqc_reference
[2023-03-17 06:30:51,355] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 06:30:51,355] [INFO] Task started: Prodigal
[2023-03-17 06:30:51,356] [INFO] Running command: cat /var/lib/cwl/stgd9cf7ccb-466b-4962-8fc2-b6038b0fc238/OceanDNA-b8887.fa | prodigal -d OceanDNA-b8887/cds.fna -a OceanDNA-b8887/protein.faa -g 11 -q > /dev/null
[2023-03-17 06:30:55,050] [INFO] Task succeeded: Prodigal
[2023-03-17 06:30:55,051] [INFO] Task started: HMMsearch
[2023-03-17 06:30:55,051] [INFO] Running command: hmmsearch --tblout OceanDNA-b8887/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg911efb5c-c7ce-4354-a4ca-3df2be41ba6a/dqc_reference/reference_markers.hmm OceanDNA-b8887/protein.faa > /dev/null
[2023-03-17 06:30:55,191] [INFO] Task succeeded: HMMsearch
[2023-03-17 06:30:55,191] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd9cf7ccb-466b-4962-8fc2-b6038b0fc238/OceanDNA-b8887.fa]
[2023-03-17 06:30:55,199] [INFO] Query marker FASTA was written to OceanDNA-b8887/markers.fasta
[2023-03-17 06:30:55,200] [INFO] Task started: Blastn
[2023-03-17 06:30:55,200] [INFO] Running command: blastn -query OceanDNA-b8887/markers.fasta -db /var/lib/cwl/stg911efb5c-c7ce-4354-a4ca-3df2be41ba6a/dqc_reference/reference_markers.fasta -out OceanDNA-b8887/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 06:30:57,039] [INFO] Task succeeded: Blastn
[2023-03-17 06:30:57,040] [INFO] Selected 29 target genomes.
[2023-03-17 06:30:57,040] [INFO] Target genome list was writen to OceanDNA-b8887/target_genomes.txt
[2023-03-17 06:30:57,055] [INFO] Task started: fastANI
[2023-03-17 06:30:57,056] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9cf7ccb-466b-4962-8fc2-b6038b0fc238/OceanDNA-b8887.fa --refList OceanDNA-b8887/target_genomes.txt --output OceanDNA-b8887/fastani_result.tsv --threads 1
[2023-03-17 06:31:13,018] [INFO] Task succeeded: fastANI
[2023-03-17 06:31:13,019] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg911efb5c-c7ce-4354-a4ca-3df2be41ba6a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 06:31:13,019] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg911efb5c-c7ce-4354-a4ca-3df2be41ba6a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 06:31:13,019] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 06:31:13,019] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 06:31:13,019] [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 06:31:13,019] [INFO] DFAST Taxonomy check result was written to OceanDNA-b8887/tc_result.tsv
[2023-03-17 06:31:13,019] [INFO] ===== Taxonomy check completed =====
[2023-03-17 06:31:13,020] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 06:31:13,020] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg911efb5c-c7ce-4354-a4ca-3df2be41ba6a/dqc_reference/checkm_data
[2023-03-17 06:31:13,022] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 06:31:13,025] [INFO] Task started: CheckM
[2023-03-17 06:31:13,025] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b8887/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b8887/checkm_input OceanDNA-b8887/checkm_result
[2023-03-17 06:31:28,933] [INFO] Task succeeded: CheckM
[2023-03-17 06:31:28,934] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.01%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 06:31:28,935] [INFO] ===== Completeness check finished =====
[2023-03-17 06:31:28,936] [INFO] ===== Start GTDB Search =====
[2023-03-17 06:31:28,936] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b8887/markers.fasta)
[2023-03-17 06:31:28,936] [INFO] Task started: Blastn
[2023-03-17 06:31:28,936] [INFO] Running command: blastn -query OceanDNA-b8887/markers.fasta -db /var/lib/cwl/stg911efb5c-c7ce-4354-a4ca-3df2be41ba6a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b8887/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 06:31:29,634] [INFO] Task succeeded: Blastn
[2023-03-17 06:31:29,635] [INFO] Selected 10 target genomes.
[2023-03-17 06:31:29,635] [INFO] Target genome list was writen to OceanDNA-b8887/target_genomes_gtdb.txt
[2023-03-17 06:31:29,757] [INFO] Task started: fastANI
[2023-03-17 06:31:29,757] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9cf7ccb-466b-4962-8fc2-b6038b0fc238/OceanDNA-b8887.fa --refList OceanDNA-b8887/target_genomes_gtdb.txt --output OceanDNA-b8887/fastani_result_gtdb.tsv --threads 1
[2023-03-17 06:31:31,466] [INFO] Task succeeded: fastANI
[2023-03-17 06:31:31,471] [INFO] Found 7 fastANI hits (2 hits with ANI > circumscription radius)
[2023-03-17 06:31:31,472] [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_902595555.1	s__MED-G14 sp902595555	98.0013	103	112	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	96.27	95.29	0.86	0.83	8	inconclusive
GCA_902574335.1	s__MED-G14 sp902574335	95.8067	60	112	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_902622575.1	s__MED-G14 sp902622575	82.4058	75	112	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003331885.1	s__MED-G14 sp003331885	79.9766	56	112	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	96.85	96.85	0.80	0.80	2	-
GCA_902535165.1	s__MED-G14 sp902535165	79.3836	64	112	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902546095.1	s__MED-G14 sp902546095	79.2777	57	112	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902597545.1	s__MED-G14 sp902597545	79.023	79	112	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G14	95.0	96.96	95.61	0.87	0.83	5	-
--------------------------------------------------------------------------------
[2023-03-17 06:31:31,472] [INFO] GTDB search result was written to OceanDNA-b8887/result_gtdb.tsv
[2023-03-17 06:31:31,472] [INFO] ===== GTDB Search completed =====
[2023-03-17 06:31:31,473] [INFO] DFAST_QC result json was written to OceanDNA-b8887/dqc_result.json
[2023-03-17 06:31:31,473] [INFO] DFAST_QC completed!
[2023-03-17 06:31:31,473] [INFO] Total running time: 0h0m42s