[2023-03-15 03:02:04,959] [INFO] DFAST_QC pipeline started.
[2023-03-15 03:02:04,959] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 03:02:04,960] [INFO] DQC Reference Directory: /var/lib/cwl/stgf7bea9c3-c576-44f0-bc2f-405689dc49c2/dqc_reference
[2023-03-15 03:02:06,575] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 03:02:06,576] [INFO] Task started: Prodigal
[2023-03-15 03:02:06,576] [INFO] Running command: cat /var/lib/cwl/stg3455659a-b859-4d80-a538-807e85e5d02a/OceanDNA-b22127.fa | prodigal -d OceanDNA-b22127/cds.fna -a OceanDNA-b22127/protein.faa -g 11 -q > /dev/null
[2023-03-15 03:02:22,810] [INFO] Task succeeded: Prodigal
[2023-03-15 03:02:22,810] [INFO] Task started: HMMsearch
[2023-03-15 03:02:22,810] [INFO] Running command: hmmsearch --tblout OceanDNA-b22127/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf7bea9c3-c576-44f0-bc2f-405689dc49c2/dqc_reference/reference_markers.hmm OceanDNA-b22127/protein.faa > /dev/null
[2023-03-15 03:02:23,003] [INFO] Task succeeded: HMMsearch
[2023-03-15 03:02:23,003] [INFO] Found 6/6 markers.
[2023-03-15 03:02:23,023] [INFO] Query marker FASTA was written to OceanDNA-b22127/markers.fasta
[2023-03-15 03:02:23,023] [INFO] Task started: Blastn
[2023-03-15 03:02:23,023] [INFO] Running command: blastn -query OceanDNA-b22127/markers.fasta -db /var/lib/cwl/stgf7bea9c3-c576-44f0-bc2f-405689dc49c2/dqc_reference/reference_markers.fasta -out OceanDNA-b22127/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:02:23,542] [INFO] Task succeeded: Blastn
[2023-03-15 03:02:23,543] [INFO] Selected 22 target genomes.
[2023-03-15 03:02:23,543] [INFO] Target genome list was writen to OceanDNA-b22127/target_genomes.txt
[2023-03-15 03:02:23,558] [INFO] Task started: fastANI
[2023-03-15 03:02:23,558] [INFO] Running command: fastANI --query /var/lib/cwl/stg3455659a-b859-4d80-a538-807e85e5d02a/OceanDNA-b22127.fa --refList OceanDNA-b22127/target_genomes.txt --output OceanDNA-b22127/fastani_result.tsv --threads 1
[2023-03-15 03:02:39,063] [INFO] Task succeeded: fastANI
[2023-03-15 03:02:39,064] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf7bea9c3-c576-44f0-bc2f-405689dc49c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 03:02:39,064] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf7bea9c3-c576-44f0-bc2f-405689dc49c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 03:02:39,064] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 03:02:39,064] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 03:02:39,064] [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 03:02:39,064] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22127/tc_result.tsv
[2023-03-15 03:02:39,064] [INFO] ===== Taxonomy check completed =====
[2023-03-15 03:02:39,064] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 03:02:39,065] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf7bea9c3-c576-44f0-bc2f-405689dc49c2/dqc_reference/checkm_data
[2023-03-15 03:02:39,067] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 03:02:39,075] [INFO] Task started: CheckM
[2023-03-15 03:02:39,075] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22127/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22127/checkm_input OceanDNA-b22127/checkm_result
[2023-03-15 03:03:23,498] [INFO] Task succeeded: CheckM
[2023-03-15 03:03:23,498] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 03:03:23,501] [INFO] ===== Completeness check finished =====
[2023-03-15 03:03:23,501] [INFO] ===== Start GTDB Search =====
[2023-03-15 03:03:23,501] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22127/markers.fasta)
[2023-03-15 03:03:23,502] [INFO] Task started: Blastn
[2023-03-15 03:03:23,502] [INFO] Running command: blastn -query OceanDNA-b22127/markers.fasta -db /var/lib/cwl/stgf7bea9c3-c576-44f0-bc2f-405689dc49c2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22127/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:03:24,230] [INFO] Task succeeded: Blastn
[2023-03-15 03:03:24,232] [INFO] Selected 12 target genomes.
[2023-03-15 03:03:24,233] [INFO] Target genome list was writen to OceanDNA-b22127/target_genomes_gtdb.txt
[2023-03-15 03:03:24,245] [INFO] Task started: fastANI
[2023-03-15 03:03:24,246] [INFO] Running command: fastANI --query /var/lib/cwl/stg3455659a-b859-4d80-a538-807e85e5d02a/OceanDNA-b22127.fa --refList OceanDNA-b22127/target_genomes_gtdb.txt --output OceanDNA-b22127/fastani_result_gtdb.tsv --threads 1
[2023-03-15 03:03:30,126] [INFO] Task succeeded: fastANI
[2023-03-15 03:03:30,131] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 03:03:30,131] [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_903961015.1	s__F1-60-MAGs104 sp903961015	94.3206	630	786	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__F1-60-MAGs104	95.0	99.31	98.85	0.88	0.85	12	-
GCA_005792145.1	s__F1-60-MAGs104 sp005792145	87.4316	607	786	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__F1-60-MAGs104	95.0	99.70	99.55	0.92	0.92	5	-
GCA_903919715.1	s__F1-60-MAGs104 sp903919715	81.4314	481	786	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__F1-60-MAGs104	95.0	99.88	99.87	0.97	0.95	5	-
GCA_009691725.1	s__F1-60-MAGs104 sp009691725	77.1332	104	786	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__F1-60-MAGs104	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009691705.1	s__F1-60-MAGs104 sp009691705	76.9726	100	786	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__F1-60-MAGs104	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005799205.1	s__F1-60-MAGs104 sp005799205	76.4659	57	786	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__F1-60-MAGs104	95.0	99.46	99.39	0.84	0.83	4	-
--------------------------------------------------------------------------------
[2023-03-15 03:03:30,132] [INFO] GTDB search result was written to OceanDNA-b22127/result_gtdb.tsv
[2023-03-15 03:03:30,132] [INFO] ===== GTDB Search completed =====
[2023-03-15 03:03:30,133] [INFO] DFAST_QC result json was written to OceanDNA-b22127/dqc_result.json
[2023-03-15 03:03:30,134] [INFO] DFAST_QC completed!
[2023-03-15 03:03:30,134] [INFO] Total running time: 0h1m25s