[2023-03-18 07:06:19,983] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:06:19,983] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:06:19,983] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e3db482-adb6-43e4-8053-a0e9c9ab2d03/dqc_reference
[2023-03-18 07:06:21,100] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:06:21,101] [INFO] Task started: Prodigal
[2023-03-18 07:06:21,101] [INFO] Running command: cat /var/lib/cwl/stgec9a8cad-81ea-4a90-9f16-7af508df74ff/OceanDNA-b32565.fa | prodigal -d OceanDNA-b32565/cds.fna -a OceanDNA-b32565/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:06:28,304] [INFO] Task succeeded: Prodigal
[2023-03-18 07:06:28,304] [INFO] Task started: HMMsearch
[2023-03-18 07:06:28,304] [INFO] Running command: hmmsearch --tblout OceanDNA-b32565/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e3db482-adb6-43e4-8053-a0e9c9ab2d03/dqc_reference/reference_markers.hmm OceanDNA-b32565/protein.faa > /dev/null
[2023-03-18 07:06:28,489] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:06:28,490] [INFO] Found 6/6 markers.
[2023-03-18 07:06:28,500] [INFO] Query marker FASTA was written to OceanDNA-b32565/markers.fasta
[2023-03-18 07:06:28,500] [INFO] Task started: Blastn
[2023-03-18 07:06:28,500] [INFO] Running command: blastn -query OceanDNA-b32565/markers.fasta -db /var/lib/cwl/stg5e3db482-adb6-43e4-8053-a0e9c9ab2d03/dqc_reference/reference_markers.fasta -out OceanDNA-b32565/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:06:29,002] [INFO] Task succeeded: Blastn
[2023-03-18 07:06:29,003] [INFO] Selected 20 target genomes.
[2023-03-18 07:06:29,003] [INFO] Target genome list was writen to OceanDNA-b32565/target_genomes.txt
[2023-03-18 07:06:29,013] [INFO] Task started: fastANI
[2023-03-18 07:06:29,013] [INFO] Running command: fastANI --query /var/lib/cwl/stgec9a8cad-81ea-4a90-9f16-7af508df74ff/OceanDNA-b32565.fa --refList OceanDNA-b32565/target_genomes.txt --output OceanDNA-b32565/fastani_result.tsv --threads 1
[2023-03-18 07:06:36,901] [INFO] Task succeeded: fastANI
[2023-03-18 07:06:36,902] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e3db482-adb6-43e4-8053-a0e9c9ab2d03/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:06:36,902] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e3db482-adb6-43e4-8053-a0e9c9ab2d03/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:06:36,902] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:06:36,902] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 07:06:36,902] [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
--------------------------------------------------------------------------------
[2023-03-18 07:06:36,902] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32565/tc_result.tsv
[2023-03-18 07:06:36,902] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:06:36,902] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:06:36,903] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e3db482-adb6-43e4-8053-a0e9c9ab2d03/dqc_reference/checkm_data
[2023-03-18 07:06:36,905] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:06:36,908] [INFO] Task started: CheckM
[2023-03-18 07:06:36,908] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32565/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32565/checkm_input OceanDNA-b32565/checkm_result
[2023-03-18 07:07:00,103] [INFO] Task succeeded: CheckM
[2023-03-18 07:07:00,103] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 07:07:00,105] [INFO] ===== Completeness check finished =====
[2023-03-18 07:07:00,105] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:07:00,105] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32565/markers.fasta)
[2023-03-18 07:07:00,106] [INFO] Task started: Blastn
[2023-03-18 07:07:00,106] [INFO] Running command: blastn -query OceanDNA-b32565/markers.fasta -db /var/lib/cwl/stg5e3db482-adb6-43e4-8053-a0e9c9ab2d03/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32565/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:07:00,847] [INFO] Task succeeded: Blastn
[2023-03-18 07:07:00,848] [INFO] Selected 20 target genomes.
[2023-03-18 07:07:00,848] [INFO] Target genome list was writen to OceanDNA-b32565/target_genomes_gtdb.txt
[2023-03-18 07:07:01,294] [INFO] Task started: fastANI
[2023-03-18 07:07:01,294] [INFO] Running command: fastANI --query /var/lib/cwl/stgec9a8cad-81ea-4a90-9f16-7af508df74ff/OceanDNA-b32565.fa --refList OceanDNA-b32565/target_genomes_gtdb.txt --output OceanDNA-b32565/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:07:05,593] [INFO] Task succeeded: fastANI
[2023-03-18 07:07:05,601] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 07:07:05,601] [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_002167825.1	s__TMED13 sp002167825	94.7736	395	471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__TMED13	95.0	100.00	100.00	0.99	0.99	2	-
GCA_902595755.1	s__TMED13 sp902595755	85.1663	362	471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__TMED13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902537615.1	s__GCA-002690875 sp902537615	76.7992	81	471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__GCA-002690875	95.0	96.75	96.75	0.77	0.77	2	-
GCA_902617375.1	s__GCA-2691245 sp902617375	76.7325	99	471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__GCA-2691245	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902563305.1	s__GCA-2691245 sp902563305	76.6647	104	471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__GCA-2691245	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002689325.1	s__GCA-002690875 sp002689325	76.4724	83	471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__GCA-002690875	95.0	100.00	100.00	0.99	0.99	2	-
GCA_902547955.1	s__MED-G10 sp902547955	76.4331	83	471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__MED-G10	95.0	97.61	97.06	0.82	0.80	5	-
GCA_902524895.1	s__SP4073 sp902524895	76.3349	50	471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__SP4073	95.0	96.76	96.76	0.88	0.88	2	-
GCA_902590895.1	s__MED-G10 sp902590895	76.1285	68	471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__MED-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902530985.1	s__GCA-2691245 sp902530985	76.0872	66	471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__GCA-2691245	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002167215.1	s__GCA-2691245 sp002167215	76.0367	73	471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__GCA-2691245	95.0	97.98	96.11	0.71	0.71	3	-
GCA_002712255.1	s__MED-G10 sp002712255	75.9739	70	471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__MED-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002711625.1	s__GCA-2711625 sp002711625	75.9424	61	471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED127;f__TMED127;g__GCA-2711625	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 07:07:05,601] [INFO] GTDB search result was written to OceanDNA-b32565/result_gtdb.tsv
[2023-03-18 07:07:05,602] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:07:05,602] [INFO] DFAST_QC result json was written to OceanDNA-b32565/dqc_result.json
[2023-03-18 07:07:05,603] [INFO] DFAST_QC completed!
[2023-03-18 07:07:05,603] [INFO] Total running time: 0h0m46s