[2023-03-16 16:16:25,431] [INFO] DFAST_QC pipeline started.
[2023-03-16 16:16:25,432] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 16:16:25,432] [INFO] DQC Reference Directory: /var/lib/cwl/stg3f929909-1102-4969-90bc-0702b94eae32/dqc_reference
[2023-03-16 16:16:26,607] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 16:16:26,607] [INFO] Task started: Prodigal
[2023-03-16 16:16:26,607] [INFO] Running command: cat /var/lib/cwl/stge78b05e2-2ef4-404c-8137-e17fdcf28f9b/OceanDNA-b20950.fa | prodigal -d OceanDNA-b20950/cds.fna -a OceanDNA-b20950/protein.faa -g 11 -q > /dev/null
[2023-03-16 16:17:07,614] [INFO] Task succeeded: Prodigal
[2023-03-16 16:17:07,614] [INFO] Task started: HMMsearch
[2023-03-16 16:17:07,614] [INFO] Running command: hmmsearch --tblout OceanDNA-b20950/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3f929909-1102-4969-90bc-0702b94eae32/dqc_reference/reference_markers.hmm OceanDNA-b20950/protein.faa > /dev/null
[2023-03-16 16:17:07,844] [INFO] Task succeeded: HMMsearch
[2023-03-16 16:17:07,844] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge78b05e2-2ef4-404c-8137-e17fdcf28f9b/OceanDNA-b20950.fa]
[2023-03-16 16:17:07,886] [INFO] Query marker FASTA was written to OceanDNA-b20950/markers.fasta
[2023-03-16 16:17:07,888] [INFO] Task started: Blastn
[2023-03-16 16:17:07,888] [INFO] Running command: blastn -query OceanDNA-b20950/markers.fasta -db /var/lib/cwl/stg3f929909-1102-4969-90bc-0702b94eae32/dqc_reference/reference_markers.fasta -out OceanDNA-b20950/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:17:08,454] [INFO] Task succeeded: Blastn
[2023-03-16 16:17:08,455] [INFO] Selected 35 target genomes.
[2023-03-16 16:17:08,455] [INFO] Target genome list was writen to OceanDNA-b20950/target_genomes.txt
[2023-03-16 16:17:08,473] [INFO] Task started: fastANI
[2023-03-16 16:17:08,473] [INFO] Running command: fastANI --query /var/lib/cwl/stge78b05e2-2ef4-404c-8137-e17fdcf28f9b/OceanDNA-b20950.fa --refList OceanDNA-b20950/target_genomes.txt --output OceanDNA-b20950/fastani_result.tsv --threads 1
[2023-03-16 16:17:33,630] [INFO] Task succeeded: fastANI
[2023-03-16 16:17:33,630] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3f929909-1102-4969-90bc-0702b94eae32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 16:17:33,630] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3f929909-1102-4969-90bc-0702b94eae32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 16:17:33,640] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 16:17:33,640] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 16:17:33,640] [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
Myxococcus fulvus	strain=NBRC 100333	GCA_007991095.1	33	33	type	True	74.994	83	856	95	below_threshold
Myxococcus fulvus	strain=DSM 16525	GCA_900111765.1	33	33	type	True	74.988	84	856	95	below_threshold
Roseomonas rhizosphaerae	strain=YW11	GCA_002631185.1	1335062	1335062	type	True	74.7496	50	856	95	below_threshold
Sphaerotilus natans subsp. natans	strain=DSM 6575	GCA_000689195.1	882627	34103	type	True	74.7101	56	856	95	below_threshold
Sphaerotilus natans	strain=ATCC 13338	GCA_900156335.1	34103	34103	type	True	74.7095	57	856	95	below_threshold
Catellatospora chokoriensis	strain=2-25(1)	GCA_011297315.1	310353	310353	type	True	74.682	90	856	95	below_threshold
Roseomonas coralli	strain=M0104	GCA_009829925.1	2545983	2545983	type	True	74.6797	53	856	95	below_threshold
Xylophilus rhododendri	strain=KACC 21265	GCA_009906855.1	2697032	2697032	type	True	74.6667	73	856	95	below_threshold
Actinoplanes lichenicola	strain=LDG1-01	GCA_016785085.1	2802976	2802976	type	True	74.6503	86	856	95	below_threshold
Catellatospora paridis	strain=NEAU-CL2	GCA_009720365.1	1617086	1617086	type	True	74.6269	94	856	95	below_threshold
Catellatospora vulcania	strain=NEAU-JM1	GCA_009720385.1	1460450	1460450	type	True	74.6219	100	856	95	below_threshold
Azohydromonas lata	strain=NBRC 102462	GCA_001571085.1	45677	45677	type	True	74.6215	73	856	95	below_threshold
Actinoplanes ianthinogenes	strain=NBRC 13996	GCA_018324205.1	122358	122358	type	True	74.6001	100	856	95	below_threshold
Amycolatopsis rifamycinica	strain=DSM 46095	GCA_000695625.1	287986	287986	type	True	74.5755	78	856	95	below_threshold
Geodermatophilus tzadiensis	strain=DSM 45416	GCA_003002915.1	1137988	1137988	type	True	74.5547	80	856	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 16:17:33,640] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20950/tc_result.tsv
[2023-03-16 16:17:33,640] [INFO] ===== Taxonomy check completed =====
[2023-03-16 16:17:33,640] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 16:17:33,641] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3f929909-1102-4969-90bc-0702b94eae32/dqc_reference/checkm_data
[2023-03-16 16:17:33,641] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 16:17:33,648] [INFO] Task started: CheckM
[2023-03-16 16:17:33,648] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20950/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20950/checkm_input OceanDNA-b20950/checkm_result
[2023-03-16 16:19:19,570] [INFO] Task succeeded: CheckM
[2023-03-16 16:19:19,570] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 34.75%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 16:19:19,574] [INFO] ===== Completeness check finished =====
[2023-03-16 16:19:19,574] [INFO] ===== Start GTDB Search =====
[2023-03-16 16:19:19,574] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20950/markers.fasta)
[2023-03-16 16:19:19,576] [INFO] Task started: Blastn
[2023-03-16 16:19:19,576] [INFO] Running command: blastn -query OceanDNA-b20950/markers.fasta -db /var/lib/cwl/stg3f929909-1102-4969-90bc-0702b94eae32/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20950/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:19:20,427] [INFO] Task succeeded: Blastn
[2023-03-16 16:19:20,428] [INFO] Selected 31 target genomes.
[2023-03-16 16:19:20,428] [INFO] Target genome list was writen to OceanDNA-b20950/target_genomes_gtdb.txt
[2023-03-16 16:19:21,653] [INFO] Task started: fastANI
[2023-03-16 16:19:21,653] [INFO] Running command: fastANI --query /var/lib/cwl/stge78b05e2-2ef4-404c-8137-e17fdcf28f9b/OceanDNA-b20950.fa --refList OceanDNA-b20950/target_genomes_gtdb.txt --output OceanDNA-b20950/fastani_result_gtdb.tsv --threads 1
[2023-03-16 16:19:59,257] [INFO] Task succeeded: fastANI
[2023-03-16 16:19:59,268] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 16:19:59,268] [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_003694325.1	s__J125 sp003694325	75.9409	108	856	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__UBA2385;g__J125	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016717595.1	s__JADKFE01 sp016717595	75.8905	125	856	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__CAJQPC01;g__JADKFE01	95.0	98.32	98.16	0.91	0.88	3	-
GCA_016875315.1	s__SXON01 sp016875315	75.8646	98	856	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__SXON01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016875435.1	s__SXON01 sp016875435	75.7596	94	856	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__SXON01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016845285.1	s__BH17 sp016845285	75.7277	95	856	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__UBA2385;g__BH17	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401435.1	s__M30B51 sp018401435	75.7276	154	856	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__UBA2385;g__M30B51	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015489145.1	s__S143-5 sp015489145	75.6985	140	856	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__UBA2385;g__S143-5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002343455.1	s__UBA2385 sp002343455	75.6934	184	856	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__UBA2385;g__UBA2385	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903875225.1	s__CAIUMM01 sp903875225	75.6382	93	856	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__CAIUMM01	95.0	99.62	99.43	0.93	0.90	4	-
GCA_903959175.1	s__CAJBVW01 sp903959175	75.5656	130	856	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__CAJBVW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006226595.1	s__M1803 sp006226595	75.5297	112	856	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__GCA-2862545;g__M1803	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009692585.1	s__SXON01 sp009692585	75.4553	71	856	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__SXON01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016792625.1	s__JAEUKK01 sp016792625	75.3069	141	856	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__UBA2385;g__JAEUKK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903844155.1	s__CAIUMM01 sp903844155	75.0471	89	856	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__CAIUMM01	95.0	99.98	99.97	0.97	0.97	4	-
GCA_016714285.1	s__Nannocystis sp016714285	74.79	108	856	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Nannocystis	95.0	99.25	99.25	0.96	0.96	2	-
GCA_016218545.1	s__JACQWX01 sp016218545	74.7783	50	856	d__Bacteria;p__Elusimicrobiota;c__Elusimicrobia;o__UBA1565;f__UBA9628;g__JACQWX01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016785085.1	s__Actinoplanes sp016785085	74.6269	86	856	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000695625.1	s__Amycolatopsis rifamycinica	74.57	79	856	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 16:19:59,268] [INFO] GTDB search result was written to OceanDNA-b20950/result_gtdb.tsv
[2023-03-16 16:19:59,268] [INFO] ===== GTDB Search completed =====
[2023-03-16 16:19:59,270] [INFO] DFAST_QC result json was written to OceanDNA-b20950/dqc_result.json
[2023-03-16 16:19:59,270] [INFO] DFAST_QC completed!
[2023-03-16 16:19:59,270] [INFO] Total running time: 0h3m34s