[2023-03-18 02:53:05,585] [INFO] DFAST_QC pipeline started.
[2023-03-18 02:53:05,585] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 02:53:05,585] [INFO] DQC Reference Directory: /var/lib/cwl/stg4dcb6e91-cbca-4e0e-82be-077337e61480/dqc_reference
[2023-03-18 02:53:07,189] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 02:53:07,190] [INFO] Task started: Prodigal
[2023-03-18 02:53:07,190] [INFO] Running command: cat /var/lib/cwl/stgab641eed-7eb8-4d52-a980-97fac10c2bdf/OceanDNA-b20894.fa | prodigal -d OceanDNA-b20894/cds.fna -a OceanDNA-b20894/protein.faa -g 11 -q > /dev/null
[2023-03-18 02:53:31,163] [INFO] Task succeeded: Prodigal
[2023-03-18 02:53:31,163] [INFO] Task started: HMMsearch
[2023-03-18 02:53:31,163] [INFO] Running command: hmmsearch --tblout OceanDNA-b20894/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4dcb6e91-cbca-4e0e-82be-077337e61480/dqc_reference/reference_markers.hmm OceanDNA-b20894/protein.faa > /dev/null
[2023-03-18 02:53:31,420] [INFO] Task succeeded: HMMsearch
[2023-03-18 02:53:31,421] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgab641eed-7eb8-4d52-a980-97fac10c2bdf/OceanDNA-b20894.fa]
[2023-03-18 02:53:31,455] [INFO] Query marker FASTA was written to OceanDNA-b20894/markers.fasta
[2023-03-18 02:53:31,455] [INFO] Task started: Blastn
[2023-03-18 02:53:31,455] [INFO] Running command: blastn -query OceanDNA-b20894/markers.fasta -db /var/lib/cwl/stg4dcb6e91-cbca-4e0e-82be-077337e61480/dqc_reference/reference_markers.fasta -out OceanDNA-b20894/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:53:32,107] [INFO] Task succeeded: Blastn
[2023-03-18 02:53:32,108] [INFO] Selected 30 target genomes.
[2023-03-18 02:53:32,108] [INFO] Target genome list was writen to OceanDNA-b20894/target_genomes.txt
[2023-03-18 02:53:32,122] [INFO] Task started: fastANI
[2023-03-18 02:53:32,123] [INFO] Running command: fastANI --query /var/lib/cwl/stgab641eed-7eb8-4d52-a980-97fac10c2bdf/OceanDNA-b20894.fa --refList OceanDNA-b20894/target_genomes.txt --output OceanDNA-b20894/fastani_result.tsv --threads 1
[2023-03-18 02:53:52,598] [INFO] Task succeeded: fastANI
[2023-03-18 02:53:52,598] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4dcb6e91-cbca-4e0e-82be-077337e61480/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:53:52,598] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4dcb6e91-cbca-4e0e-82be-077337e61480/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:53:52,602] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 02:53:52,602] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 02:53:52,602] [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
Lujinxingia vulgaris	strain=TMQ4	GCA_007997015.1	2600176	2600176	type	True	75.8725	67	1060	95	below_threshold
Persicimonas caeni	strain=YN101	GCA_006517175.1	2292766	2292766	type	True	75.4652	98	1060	95	below_threshold
Persicimonas caeni	strain=YN101	GCA_007993775.1	2292766	2292766	type	True	75.4622	98	1060	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 02:53:52,899] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20894/tc_result.tsv
[2023-03-18 02:53:52,899] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:53:52,899] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:53:52,899] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4dcb6e91-cbca-4e0e-82be-077337e61480/dqc_reference/checkm_data
[2023-03-18 02:53:52,900] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:53:52,919] [INFO] Task started: CheckM
[2023-03-18 02:53:52,919] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20894/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20894/checkm_input OceanDNA-b20894/checkm_result
[2023-03-18 02:54:54,036] [INFO] Task succeeded: CheckM
[2023-03-18 02:54:54,036] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.89%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 02:54:54,040] [INFO] ===== Completeness check finished =====
[2023-03-18 02:54:54,040] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:54:54,040] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20894/markers.fasta)
[2023-03-18 02:54:54,040] [INFO] Task started: Blastn
[2023-03-18 02:54:54,040] [INFO] Running command: blastn -query OceanDNA-b20894/markers.fasta -db /var/lib/cwl/stg4dcb6e91-cbca-4e0e-82be-077337e61480/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20894/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:54:55,143] [INFO] Task succeeded: Blastn
[2023-03-18 02:54:55,143] [INFO] Selected 36 target genomes.
[2023-03-18 02:54:55,144] [INFO] Target genome list was writen to OceanDNA-b20894/target_genomes_gtdb.txt
[2023-03-18 02:54:55,462] [INFO] Task started: fastANI
[2023-03-18 02:54:55,462] [INFO] Running command: fastANI --query /var/lib/cwl/stgab641eed-7eb8-4d52-a980-97fac10c2bdf/OceanDNA-b20894.fa --refList OceanDNA-b20894/target_genomes_gtdb.txt --output OceanDNA-b20894/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:55:21,906] [INFO] Task succeeded: fastANI
[2023-03-18 02:55:21,912] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 02:55:21,913] [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
GCF_004005565.1	s__Lujinxingia sediminis	76.7319	70	1060	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__Lujinxingia	95.0	98.95	98.95	0.97	0.97	3	-
GCA_013697635.1	s__JACCWM01 sp013697635	75.8768	88	1060	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__JACCWM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007997015.1	s__Lujinxingia sp007997015	75.8725	67	1060	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__Lujinxingia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007997005.1	s__Lujinxingia sp007997005	75.7738	88	1060	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__Lujinxingia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006517175.1	s__Persicimonas caeni	75.4548	99	1060	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__Persicimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900696455.1	s__UBA2376 sp900696455	75.0161	64	1060	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	98.40	97.29	0.91	0.90	3	-
GCA_005804885.1	s__SYOX01 sp005804885	74.9954	71	1060	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__GCA-2716585;g__SYOX01	95.0	99.96	99.96	0.96	0.96	2	-
GCA_903845045.1	s__SCUS01 sp903845045	74.9728	50	1060	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Ga0077539;g__SCUS01	95.0	99.02	99.02	0.83	0.83	2	-
GCA_016794525.1	s__UBA2376 sp016794525	74.9642	60	1060	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016706685.1	s__JADJJE01 sp016706685	74.7387	57	1060	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__JADJJE01	95.0	99.15	99.06	0.93	0.90	7	-
--------------------------------------------------------------------------------
[2023-03-18 02:55:21,913] [INFO] GTDB search result was written to OceanDNA-b20894/result_gtdb.tsv
[2023-03-18 02:55:21,913] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:55:21,914] [INFO] DFAST_QC result json was written to OceanDNA-b20894/dqc_result.json
[2023-03-18 02:55:21,914] [INFO] DFAST_QC completed!
[2023-03-18 02:55:21,914] [INFO] Total running time: 0h2m16s