[2023-03-15 21:01:44,394] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:01:44,395] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:01:44,395] [INFO] DQC Reference Directory: /var/lib/cwl/stg89da99b9-6f33-4f51-9c57-9c43426d0981/dqc_reference
[2023-03-15 21:01:45,596] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:01:45,597] [INFO] Task started: Prodigal
[2023-03-15 21:01:45,597] [INFO] Running command: cat /var/lib/cwl/stg7aa99956-07d6-4fe0-9dd0-df6f6613352a/OceanDNA-b8550.fa | prodigal -d OceanDNA-b8550/cds.fna -a OceanDNA-b8550/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:01:50,589] [INFO] Task succeeded: Prodigal
[2023-03-15 21:01:50,590] [INFO] Task started: HMMsearch
[2023-03-15 21:01:50,590] [INFO] Running command: hmmsearch --tblout OceanDNA-b8550/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg89da99b9-6f33-4f51-9c57-9c43426d0981/dqc_reference/reference_markers.hmm OceanDNA-b8550/protein.faa > /dev/null
[2023-03-15 21:01:50,725] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:01:50,726] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg7aa99956-07d6-4fe0-9dd0-df6f6613352a/OceanDNA-b8550.fa]
[2023-03-15 21:01:50,732] [INFO] Query marker FASTA was written to OceanDNA-b8550/markers.fasta
[2023-03-15 21:01:50,733] [INFO] Task started: Blastn
[2023-03-15 21:01:50,733] [INFO] Running command: blastn -query OceanDNA-b8550/markers.fasta -db /var/lib/cwl/stg89da99b9-6f33-4f51-9c57-9c43426d0981/dqc_reference/reference_markers.fasta -out OceanDNA-b8550/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:01:51,163] [INFO] Task succeeded: Blastn
[2023-03-15 21:01:51,164] [INFO] Selected 10 target genomes.
[2023-03-15 21:01:51,164] [INFO] Target genome list was writen to OceanDNA-b8550/target_genomes.txt
[2023-03-15 21:01:51,169] [INFO] Task started: fastANI
[2023-03-15 21:01:51,170] [INFO] Running command: fastANI --query /var/lib/cwl/stg7aa99956-07d6-4fe0-9dd0-df6f6613352a/OceanDNA-b8550.fa --refList OceanDNA-b8550/target_genomes.txt --output OceanDNA-b8550/fastani_result.tsv --threads 1
[2023-03-15 21:01:56,453] [INFO] Task succeeded: fastANI
[2023-03-15 21:01:56,454] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg89da99b9-6f33-4f51-9c57-9c43426d0981/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:01:56,454] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg89da99b9-6f33-4f51-9c57-9c43426d0981/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:01:56,454] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:01:56,454] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 21:01:56,454] [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 21:01:56,454] [INFO] DFAST Taxonomy check result was written to OceanDNA-b8550/tc_result.tsv
[2023-03-15 21:01:56,454] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:01:56,455] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:01:56,455] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg89da99b9-6f33-4f51-9c57-9c43426d0981/dqc_reference/checkm_data
[2023-03-15 21:01:56,457] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:01:56,461] [INFO] Task started: CheckM
[2023-03-15 21:01:56,461] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b8550/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b8550/checkm_input OceanDNA-b8550/checkm_result
[2023-03-15 21:02:15,277] [INFO] Task succeeded: CheckM
[2023-03-15 21:02:15,278] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 21:02:15,279] [INFO] ===== Completeness check finished =====
[2023-03-15 21:02:15,279] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:02:15,279] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b8550/markers.fasta)
[2023-03-15 21:02:15,280] [INFO] Task started: Blastn
[2023-03-15 21:02:15,280] [INFO] Running command: blastn -query OceanDNA-b8550/markers.fasta -db /var/lib/cwl/stg89da99b9-6f33-4f51-9c57-9c43426d0981/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b8550/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:02:16,990] [INFO] Task succeeded: Blastn
[2023-03-15 21:02:16,991] [INFO] Selected 12 target genomes.
[2023-03-15 21:02:16,991] [INFO] Target genome list was writen to OceanDNA-b8550/target_genomes_gtdb.txt
[2023-03-15 21:02:17,554] [INFO] Task started: fastANI
[2023-03-15 21:02:17,555] [INFO] Running command: fastANI --query /var/lib/cwl/stg7aa99956-07d6-4fe0-9dd0-df6f6613352a/OceanDNA-b8550.fa --refList OceanDNA-b8550/target_genomes_gtdb.txt --output OceanDNA-b8550/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:02:20,243] [INFO] Task succeeded: fastANI
[2023-03-15 21:02:20,250] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 21:02:20,250] [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_902516925.1	s__MED-G11 sp902516925	81.0611	110	278	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902629505.1	s__MED-G11 sp902629505	80.1724	121	278	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902523665.1	s__MED-G11 sp902523665	79.7203	130	278	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902620455.1	s__MED-G11 sp902620455	79.7005	141	278	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	99.20	98.53	0.88	0.86	7	-
GCA_902622595.1	s__MED-G11 sp902622595	79.6222	159	278	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	96.81	96.16	0.93	0.91	12	-
GCA_905380995.1	s__MED-G11 sp905380995	79.3088	124	278	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018646865.1	s__MED-G11 sp014239615	79.0755	142	278	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	99.76	99.49	0.92	0.80	17	-
GCA_902509805.1	s__MED-G11 sp902509805	79.0647	94	278	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	97.79	97.79	0.58	0.58	2	-
GCA_004214015.1	s__MED-G11 sp004214015	78.9409	110	278	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	97.90	97.77	0.83	0.80	4	-
GCA_002457075.1	s__MED-G11 sp002457075	78.7917	114	278	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	98.35	98.35	0.79	0.79	2	-
GCA_016780245.1	s__MED-G11 sp016780245	78.3396	79	278	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	99.94	99.94	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2023-03-15 21:02:20,251] [INFO] GTDB search result was written to OceanDNA-b8550/result_gtdb.tsv
[2023-03-15 21:02:20,251] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:02:20,252] [INFO] DFAST_QC result json was written to OceanDNA-b8550/dqc_result.json
[2023-03-15 21:02:20,252] [INFO] DFAST_QC completed!
[2023-03-15 21:02:20,252] [INFO] Total running time: 0h0m36s