[2023-03-16 05:09:10,897] [INFO] DFAST_QC pipeline started.
[2023-03-16 05:09:10,898] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 05:09:10,898] [INFO] DQC Reference Directory: /var/lib/cwl/stg561e5fb3-8ab7-4d13-ae05-66ea52bbe93d/dqc_reference
[2023-03-16 05:09:12,018] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 05:09:12,018] [INFO] Task started: Prodigal
[2023-03-16 05:09:12,019] [INFO] Running command: cat /var/lib/cwl/stgb9c25631-e742-46da-8f81-6b618012812a/OceanDNA-b20895.fa | prodigal -d OceanDNA-b20895/cds.fna -a OceanDNA-b20895/protein.faa -g 11 -q > /dev/null
[2023-03-16 05:09:36,560] [INFO] Task succeeded: Prodigal
[2023-03-16 05:09:36,560] [INFO] Task started: HMMsearch
[2023-03-16 05:09:36,560] [INFO] Running command: hmmsearch --tblout OceanDNA-b20895/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg561e5fb3-8ab7-4d13-ae05-66ea52bbe93d/dqc_reference/reference_markers.hmm OceanDNA-b20895/protein.faa > /dev/null
[2023-03-16 05:09:36,814] [INFO] Task succeeded: HMMsearch
[2023-03-16 05:09:36,815] [INFO] Found 6/6 markers.
[2023-03-16 05:09:36,846] [INFO] Query marker FASTA was written to OceanDNA-b20895/markers.fasta
[2023-03-16 05:09:36,847] [INFO] Task started: Blastn
[2023-03-16 05:09:36,847] [INFO] Running command: blastn -query OceanDNA-b20895/markers.fasta -db /var/lib/cwl/stg561e5fb3-8ab7-4d13-ae05-66ea52bbe93d/dqc_reference/reference_markers.fasta -out OceanDNA-b20895/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:09:37,483] [INFO] Task succeeded: Blastn
[2023-03-16 05:09:37,484] [INFO] Selected 29 target genomes.
[2023-03-16 05:09:37,485] [INFO] Target genome list was writen to OceanDNA-b20895/target_genomes.txt
[2023-03-16 05:09:37,502] [INFO] Task started: fastANI
[2023-03-16 05:09:37,502] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9c25631-e742-46da-8f81-6b618012812a/OceanDNA-b20895.fa --refList OceanDNA-b20895/target_genomes.txt --output OceanDNA-b20895/fastani_result.tsv --threads 1
[2023-03-16 05:09:56,884] [INFO] Task succeeded: fastANI
[2023-03-16 05:09:56,884] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg561e5fb3-8ab7-4d13-ae05-66ea52bbe93d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 05:09:56,884] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg561e5fb3-8ab7-4d13-ae05-66ea52bbe93d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 05:09:56,891] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 05:09:56,891] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 05:09:56,891] [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	76.0174	102	1184	95	below_threshold
Lujinxingia litoralis	strain=B210	GCA_003260125.1	2211119	2211119	type	True	76.0062	66	1184	95	below_threshold
Lujinxingia sediminis	strain=SEH01	GCA_004005565.1	2480984	2480984	type	True	75.8205	88	1184	95	below_threshold
Bradymonas sediminis	strain=DSM 28820	GCA_004362595.1	1548548	1548548	type	True	75.7189	51	1184	95	below_threshold
Bradymonas sediminis	strain=FA350	GCA_003258315.1	1548548	1548548	type	True	75.7189	51	1184	95	below_threshold
Persicimonas caeni	strain=YN101	GCA_007993775.1	2292766	2292766	type	True	75.503	134	1184	95	below_threshold
Persicimonas caeni	strain=YN101	GCA_006517175.1	2292766	2292766	type	True	75.503	134	1184	95	below_threshold
Myxococcus eversor	strain=AB053B	GCA_010894455.1	2709661	2709661	type	True	74.9184	92	1184	95	below_threshold
Luteimonas huabeiensis	strain=HB2	GCA_000559025.1	1244513	1244513	type	True	74.847	55	1184	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 05:09:56,892] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20895/tc_result.tsv
[2023-03-16 05:09:56,892] [INFO] ===== Taxonomy check completed =====
[2023-03-16 05:09:56,892] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 05:09:56,892] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg561e5fb3-8ab7-4d13-ae05-66ea52bbe93d/dqc_reference/checkm_data
[2023-03-16 05:09:56,893] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 05:09:56,899] [INFO] Task started: CheckM
[2023-03-16 05:09:56,900] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20895/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20895/checkm_input OceanDNA-b20895/checkm_result
[2023-03-16 05:11:00,635] [INFO] Task succeeded: CheckM
[2023-03-16 05:11:00,635] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.61%
Contamintation: 1.39%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 05:11:00,641] [INFO] ===== Completeness check finished =====
[2023-03-16 05:11:00,641] [INFO] ===== Start GTDB Search =====
[2023-03-16 05:11:00,641] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20895/markers.fasta)
[2023-03-16 05:11:00,642] [INFO] Task started: Blastn
[2023-03-16 05:11:00,642] [INFO] Running command: blastn -query OceanDNA-b20895/markers.fasta -db /var/lib/cwl/stg561e5fb3-8ab7-4d13-ae05-66ea52bbe93d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20895/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:11:01,657] [INFO] Task succeeded: Blastn
[2023-03-16 05:11:01,659] [INFO] Selected 31 target genomes.
[2023-03-16 05:11:01,659] [INFO] Target genome list was writen to OceanDNA-b20895/target_genomes_gtdb.txt
[2023-03-16 05:11:01,717] [INFO] Task started: fastANI
[2023-03-16 05:11:01,717] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9c25631-e742-46da-8f81-6b618012812a/OceanDNA-b20895.fa --refList OceanDNA-b20895/target_genomes_gtdb.txt --output OceanDNA-b20895/fastani_result_gtdb.tsv --threads 1
[2023-03-16 05:11:26,056] [INFO] Task succeeded: fastANI
[2023-03-16 05:11:26,064] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 05:11:26,064] [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_007997015.1	s__Lujinxingia sp007997015	76.0174	102	1184	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__Lujinxingia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003260125.1	s__Lujinxingia litoralis	76.0062	66	1184	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	75.9963	119	1184	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__Lujinxingia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007120035.1	s__SKON01 sp007120035	75.9542	80	1184	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__SKON01	95.0	99.72	99.66	0.90	0.87	5	-
GCF_004005565.1	s__Lujinxingia sediminis	75.8205	88	1184	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	75.7379	95	1184	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__JACCWM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003258315.1	s__Bradymonas sediminis	75.7189	51	1184	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__Bradymonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_006517175.1	s__Persicimonas caeni	75.503	134	1184	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__Persicimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_903847385.1	s__CAINDO01 sp903847385	74.9515	85	1184	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__UBA7976;f__UBA1532;g__CAINDO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000170895.1	s__Plesiocystis pacifica	74.9092	100	1184	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Plesiocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000559025.1	s__Luteimonas huabeiensis	74.8561	54	1184	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018813065.1	s__JAHJCH01 sp018813065	74.7611	59	1184	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__UBA7976;f__UBA1532;g__JAHJCH01	95.0	99.74	99.61	0.91	0.89	3	-
GCA_016792625.1	s__JAEUKK01 sp016792625	74.6011	51	1184	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__UBA2385;g__JAEUKK01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 05:11:26,065] [INFO] GTDB search result was written to OceanDNA-b20895/result_gtdb.tsv
[2023-03-16 05:11:26,065] [INFO] ===== GTDB Search completed =====
[2023-03-16 05:11:26,067] [INFO] DFAST_QC result json was written to OceanDNA-b20895/dqc_result.json
[2023-03-16 05:11:26,068] [INFO] DFAST_QC completed!
[2023-03-16 05:11:26,068] [INFO] Total running time: 0h2m15s