[2023-03-17 13:01:51,387] [INFO] DFAST_QC pipeline started.
[2023-03-17 13:01:51,387] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 13:01:51,387] [INFO] DQC Reference Directory: /var/lib/cwl/stgd5608c31-dbea-4d5a-989c-8374d19ef9ce/dqc_reference
[2023-03-17 13:01:52,635] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 13:01:52,651] [INFO] Task started: Prodigal
[2023-03-17 13:01:52,651] [INFO] Running command: cat /var/lib/cwl/stg64268b06-23d3-4910-87ef-95f4b6e2fd31/OceanDNA-b23028.fa | prodigal -d OceanDNA-b23028/cds.fna -a OceanDNA-b23028/protein.faa -g 11 -q > /dev/null
[2023-03-17 13:02:21,998] [INFO] Task succeeded: Prodigal
[2023-03-17 13:02:21,999] [INFO] Task started: HMMsearch
[2023-03-17 13:02:21,999] [INFO] Running command: hmmsearch --tblout OceanDNA-b23028/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd5608c31-dbea-4d5a-989c-8374d19ef9ce/dqc_reference/reference_markers.hmm OceanDNA-b23028/protein.faa > /dev/null
[2023-03-17 13:02:22,247] [INFO] Task succeeded: HMMsearch
[2023-03-17 13:02:22,248] [INFO] Found 6/6 markers.
[2023-03-17 13:02:22,275] [INFO] Query marker FASTA was written to OceanDNA-b23028/markers.fasta
[2023-03-17 13:02:22,276] [INFO] Task started: Blastn
[2023-03-17 13:02:22,276] [INFO] Running command: blastn -query OceanDNA-b23028/markers.fasta -db /var/lib/cwl/stgd5608c31-dbea-4d5a-989c-8374d19ef9ce/dqc_reference/reference_markers.fasta -out OceanDNA-b23028/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 13:02:22,888] [INFO] Task succeeded: Blastn
[2023-03-17 13:02:22,889] [INFO] Selected 24 target genomes.
[2023-03-17 13:02:22,890] [INFO] Target genome list was writen to OceanDNA-b23028/target_genomes.txt
[2023-03-17 13:02:22,904] [INFO] Task started: fastANI
[2023-03-17 13:02:22,904] [INFO] Running command: fastANI --query /var/lib/cwl/stg64268b06-23d3-4910-87ef-95f4b6e2fd31/OceanDNA-b23028.fa --refList OceanDNA-b23028/target_genomes.txt --output OceanDNA-b23028/fastani_result.tsv --threads 1
[2023-03-17 13:02:39,412] [INFO] Task succeeded: fastANI
[2023-03-17 13:02:39,412] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd5608c31-dbea-4d5a-989c-8374d19ef9ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 13:02:39,412] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd5608c31-dbea-4d5a-989c-8374d19ef9ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 13:02:39,419] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 13:02:39,420] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 13:02:39,420] [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
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	75.1953	58	1550	95	below_threshold
Aurantimonas endophytica	strain=DSM 103570	GCA_014196845.1	1522175	1522175	type	True	75.1811	59	1550	95	below_threshold
Phycisphaera mikurensis	strain=NBRC 102666	GCA_000284115.1	547188	547188	type	True	75.1241	68	1550	95	below_threshold
Phycisphaera mikurensis	strain=DSM 103959	GCA_014207395.1	547188	547188	type	True	75.0673	67	1550	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	74.9434	104	1550	95	below_threshold
Paludisphaera rhizosphaereae	strain=JC665	GCA_011065895.1	2711216	2711216	type	True	74.9084	69	1550	95	below_threshold
Azospirillum thermophilum	strain=CFH 70021	GCA_003130795.1	2202148	2202148	type	True	74.8888	79	1550	95	below_threshold
Halorubrum coriense	strain=DSM 10284	GCA_000337035.1	64713	64713	type	True	74.6929	51	1550	95	below_threshold
Halegenticoccus soli	strain=SYSU A9-0	GCA_002844195.1	1985678	1985678	type	True	74.6351	50	1550	95	below_threshold
Halovivax limisalsi	strain=IBRC-M 10022	GCA_023093535.1	1453760	1453760	type	True	74.544	54	1550	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 13:02:39,420] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23028/tc_result.tsv
[2023-03-17 13:02:39,420] [INFO] ===== Taxonomy check completed =====
[2023-03-17 13:02:39,420] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 13:02:39,420] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd5608c31-dbea-4d5a-989c-8374d19ef9ce/dqc_reference/checkm_data
[2023-03-17 13:02:39,421] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 13:02:39,426] [INFO] Task started: CheckM
[2023-03-17 13:02:39,427] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23028/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23028/checkm_input OceanDNA-b23028/checkm_result
[2023-03-17 13:04:12,085] [INFO] Task succeeded: CheckM
[2023-03-17 13:04:12,085] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 13:04:12,088] [INFO] ===== Completeness check finished =====
[2023-03-17 13:04:12,088] [INFO] ===== Start GTDB Search =====
[2023-03-17 13:04:12,089] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23028/markers.fasta)
[2023-03-17 13:04:12,089] [INFO] Task started: Blastn
[2023-03-17 13:04:12,089] [INFO] Running command: blastn -query OceanDNA-b23028/markers.fasta -db /var/lib/cwl/stgd5608c31-dbea-4d5a-989c-8374d19ef9ce/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23028/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 13:04:12,975] [INFO] Task succeeded: Blastn
[2023-03-17 13:04:12,976] [INFO] Selected 17 target genomes.
[2023-03-17 13:04:12,976] [INFO] Target genome list was writen to OceanDNA-b23028/target_genomes_gtdb.txt
[2023-03-17 13:04:13,629] [INFO] Task started: fastANI
[2023-03-17 13:04:13,629] [INFO] Running command: fastANI --query /var/lib/cwl/stg64268b06-23d3-4910-87ef-95f4b6e2fd31/OceanDNA-b23028.fa --refList OceanDNA-b23028/target_genomes_gtdb.txt --output OceanDNA-b23028/fastani_result_gtdb.tsv --threads 1
[2023-03-17 13:04:27,188] [INFO] Task succeeded: fastANI
[2023-03-17 13:04:27,196] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 13:04:27,196] [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_011524785.1	s__GCA-2686945 sp011524785	78.0584	213	1550	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2686945	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007751475.1	s__GCA-2862085 sp007751475	77.1168	247	1550	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_016779205.1	s__GCA-2862085 sp016779205	77.1096	196	1550	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_007750655.1	s__Pla163 sp007750655	77.0944	264	1550	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_013360535.1	s__F1-120-MAGs118 sp013360535	77.0802	168	1550	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__F1-120-MAGs118	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862085.1	s__GCA-2862085 sp002862085	77.0011	245	1550	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_903892045.1	s__F1-120-MAGs118 sp903892045	76.9209	223	1550	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_903928115.1	s__F1-120-MAGs118 sp903928115	76.7891	181	1550	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_004357655.1	s__N075bin59 sp004357655	76.6393	202	1550	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__N075bin59	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480285.1	s__GCA-2862085 sp905480285	76.5752	200	1550	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	76.551	298	1550	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JADJNY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795205.1	s__JAEUHZ01 sp016795205	76.4587	243	1550	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_005799545.1	s__SYGM01 sp005799545	76.0336	104	1550	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__SYGM01	95.0	99.85	99.85	0.93	0.92	3	-
GCA_011526095.1	s__WYBA01 sp011526095	74.9861	207	1550	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__WYBA01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 13:04:27,197] [INFO] GTDB search result was written to OceanDNA-b23028/result_gtdb.tsv
[2023-03-17 13:04:27,197] [INFO] ===== GTDB Search completed =====
[2023-03-17 13:04:27,198] [INFO] DFAST_QC result json was written to OceanDNA-b23028/dqc_result.json
[2023-03-17 13:04:27,198] [INFO] DFAST_QC completed!
[2023-03-17 13:04:27,198] [INFO] Total running time: 0h2m36s