[2023-03-15 05:29:10,768] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:29:10,768] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:29:10,768] [INFO] DQC Reference Directory: /var/lib/cwl/stgfeaee291-bae9-4bd6-abf0-723d719f4b09/dqc_reference
[2023-03-15 05:29:12,382] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:29:12,382] [INFO] Task started: Prodigal
[2023-03-15 05:29:12,382] [INFO] Running command: cat /var/lib/cwl/stgbff9bdc8-ee8d-4ccf-b1e9-8fbaa6c3b561/OceanDNA-b23005.fa | prodigal -d OceanDNA-b23005/cds.fna -a OceanDNA-b23005/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:29:36,170] [INFO] Task succeeded: Prodigal
[2023-03-15 05:29:36,171] [INFO] Task started: HMMsearch
[2023-03-15 05:29:36,171] [INFO] Running command: hmmsearch --tblout OceanDNA-b23005/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfeaee291-bae9-4bd6-abf0-723d719f4b09/dqc_reference/reference_markers.hmm OceanDNA-b23005/protein.faa > /dev/null
[2023-03-15 05:29:36,432] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:29:36,432] [INFO] Found 6/6 markers.
[2023-03-15 05:29:36,458] [INFO] Query marker FASTA was written to OceanDNA-b23005/markers.fasta
[2023-03-15 05:29:36,458] [INFO] Task started: Blastn
[2023-03-15 05:29:36,458] [INFO] Running command: blastn -query OceanDNA-b23005/markers.fasta -db /var/lib/cwl/stgfeaee291-bae9-4bd6-abf0-723d719f4b09/dqc_reference/reference_markers.fasta -out OceanDNA-b23005/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:29:37,026] [INFO] Task succeeded: Blastn
[2023-03-15 05:29:37,027] [INFO] Selected 29 target genomes.
[2023-03-15 05:29:37,028] [INFO] Target genome list was writen to OceanDNA-b23005/target_genomes.txt
[2023-03-15 05:29:37,042] [INFO] Task started: fastANI
[2023-03-15 05:29:37,043] [INFO] Running command: fastANI --query /var/lib/cwl/stgbff9bdc8-ee8d-4ccf-b1e9-8fbaa6c3b561/OceanDNA-b23005.fa --refList OceanDNA-b23005/target_genomes.txt --output OceanDNA-b23005/fastani_result.tsv --threads 1
[2023-03-15 05:30:02,034] [INFO] Task succeeded: fastANI
[2023-03-15 05:30:02,035] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfeaee291-bae9-4bd6-abf0-723d719f4b09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:30:02,035] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfeaee291-bae9-4bd6-abf0-723d719f4b09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:30:02,035] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 05:30:02,035] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 05:30:02,035] [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 05:30:02,035] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23005/tc_result.tsv
[2023-03-15 05:30:02,036] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:30:02,036] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:30:02,036] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfeaee291-bae9-4bd6-abf0-723d719f4b09/dqc_reference/checkm_data
[2023-03-15 05:30:02,038] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:30:02,044] [INFO] Task started: CheckM
[2023-03-15 05:30:02,044] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23005/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23005/checkm_input OceanDNA-b23005/checkm_result
[2023-03-15 05:31:00,986] [INFO] Task succeeded: CheckM
[2023-03-15 05:31:00,987] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.56%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 05:31:00,989] [INFO] ===== Completeness check finished =====
[2023-03-15 05:31:00,990] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:31:00,990] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23005/markers.fasta)
[2023-03-15 05:31:00,991] [INFO] Task started: Blastn
[2023-03-15 05:31:00,991] [INFO] Running command: blastn -query OceanDNA-b23005/markers.fasta -db /var/lib/cwl/stgfeaee291-bae9-4bd6-abf0-723d719f4b09/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23005/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:31:01,829] [INFO] Task succeeded: Blastn
[2023-03-15 05:31:01,830] [INFO] Selected 28 target genomes.
[2023-03-15 05:31:01,830] [INFO] Target genome list was writen to OceanDNA-b23005/target_genomes_gtdb.txt
[2023-03-15 05:31:01,859] [INFO] Task started: fastANI
[2023-03-15 05:31:01,859] [INFO] Running command: fastANI --query /var/lib/cwl/stgbff9bdc8-ee8d-4ccf-b1e9-8fbaa6c3b561/OceanDNA-b23005.fa --refList OceanDNA-b23005/target_genomes_gtdb.txt --output OceanDNA-b23005/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:31:20,062] [INFO] Task succeeded: fastANI
[2023-03-15 05:31:20,069] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 05:31:20,069] [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_007751255.1	s__Pla86 sp007751255	77.5507	152	668	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__Pla86	95.0	100.00	100.00	1.00	1.00	2	-
GCA_007750655.1	s__Pla163 sp007750655	77.386	110	668	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__Pla163	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826945.1	s__RBC036 sp902826945	76.6376	84	668	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__RBC036	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795205.1	s__JAEUHZ01 sp016795205	76.3111	60	668	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JAEUHZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016125265.1	s__RI-242 sp016125265	76.2225	99	668	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__RI-242	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903928115.1	s__F1-120-MAGs118 sp903928115	75.988	53	668	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__F1-120-MAGs118	95.0	99.83	99.80	0.95	0.95	3	-
GCA_009691855.1	s__JABFRZ01 sp009691855	75.9828	71	668	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JABFRZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795325.1	s__WYBT01 sp016795325	75.9685	84	668	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__WYBT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903892045.1	s__F1-120-MAGs118 sp903892045	75.9242	74	668	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__F1-120-MAGs118	95.0	99.41	99.41	0.87	0.87	3	-
GCA_007751475.1	s__GCA-2862085 sp007751475	75.6301	66	668	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2862085	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016714045.1	s__JADJNY01 sp016714045	75.4644	67	668	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JADJNY01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 05:31:20,070] [INFO] GTDB search result was written to OceanDNA-b23005/result_gtdb.tsv
[2023-03-15 05:31:20,070] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:31:20,071] [INFO] DFAST_QC result json was written to OceanDNA-b23005/dqc_result.json
[2023-03-15 05:31:20,071] [INFO] DFAST_QC completed!
[2023-03-15 05:31:20,071] [INFO] Total running time: 0h2m9s