[2023-03-18 07:29:29,818] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:29:29,818] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:29:29,818] [INFO] DQC Reference Directory: /var/lib/cwl/stg9c4d6b21-0b85-48f7-a6b2-5c11eeac8351/dqc_reference
[2023-03-18 07:29:30,955] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:29:30,956] [INFO] Task started: Prodigal
[2023-03-18 07:29:30,956] [INFO] Running command: cat /var/lib/cwl/stgbfd6c23f-a239-40b6-8456-fe4d0d200723/OceanDNA-b20923.fa | prodigal -d OceanDNA-b20923/cds.fna -a OceanDNA-b20923/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:30:15,097] [INFO] Task succeeded: Prodigal
[2023-03-18 07:30:15,098] [INFO] Task started: HMMsearch
[2023-03-18 07:30:15,098] [INFO] Running command: hmmsearch --tblout OceanDNA-b20923/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9c4d6b21-0b85-48f7-a6b2-5c11eeac8351/dqc_reference/reference_markers.hmm OceanDNA-b20923/protein.faa > /dev/null
[2023-03-18 07:30:15,385] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:30:15,385] [INFO] Found 6/6 markers.
[2023-03-18 07:30:15,427] [INFO] Query marker FASTA was written to OceanDNA-b20923/markers.fasta
[2023-03-18 07:30:15,428] [INFO] Task started: Blastn
[2023-03-18 07:30:15,428] [INFO] Running command: blastn -query OceanDNA-b20923/markers.fasta -db /var/lib/cwl/stg9c4d6b21-0b85-48f7-a6b2-5c11eeac8351/dqc_reference/reference_markers.fasta -out OceanDNA-b20923/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:30:16,227] [INFO] Task succeeded: Blastn
[2023-03-18 07:30:16,227] [INFO] Selected 33 target genomes.
[2023-03-18 07:30:16,228] [INFO] Target genome list was writen to OceanDNA-b20923/target_genomes.txt
[2023-03-18 07:30:16,244] [INFO] Task started: fastANI
[2023-03-18 07:30:16,244] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfd6c23f-a239-40b6-8456-fe4d0d200723/OceanDNA-b20923.fa --refList OceanDNA-b20923/target_genomes.txt --output OceanDNA-b20923/fastani_result.tsv --threads 1
[2023-03-18 07:30:52,115] [INFO] Task succeeded: fastANI
[2023-03-18 07:30:52,116] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9c4d6b21-0b85-48f7-a6b2-5c11eeac8351/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:30:52,116] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9c4d6b21-0b85-48f7-a6b2-5c11eeac8351/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:30:52,133] [INFO] Found 33 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:30:52,133] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 07:30:52,134] [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
Sandaracinus amylolyticus	strain=DSM 53668	GCA_000737325.2	927083	927083	type	True	75.7384	696	2467	95	below_threshold
Desulfuromonas versatilis	strain=NIT-T3	GCA_019704135.1	2802975	2802975	type	True	75.2797	129	2467	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	75.273	140	2467	95	below_threshold
Polyangium spumosum	strain=DSM 14734	GCA_009649845.1	889282	889282	type	True	75.132	509	2467	95	below_threshold
Polyangium aurulentum	strain=SDU3-1	GCA_005144635.2	2567896	2567896	type	True	75.1101	490	2467	95	below_threshold
Arenimonas metalli	strain=CF5-1	GCA_000747155.1	948077	948077	type	True	75.1038	167	2467	95	below_threshold
Polyangium fumosum	strain=DSM 14668	GCA_005144585.1	889272	889272	neotype	True	75.0965	434	2467	95	below_threshold
Hankyongella ginsenosidimutans	strain=W1-2-3	GCA_005144965.1	1763828	1763828	type	True	75.0945	52	2467	95	below_threshold
Aurantimonas aggregata	strain=KCTC 52919	GCA_010500835.1	2047720	2047720	type	True	75.0669	144	2467	95	below_threshold
Azospirillum thermophilum	strain=CFH 70021	GCA_003130795.1	2202148	2202148	type	True	75.0544	260	2467	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_016583515.1	1048	1048	type	True	75.0419	154	2467	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	75.0223	162	2467	95	below_threshold
Azospirillum soli	strain=CC-LY788	GCA_017876165.1	1304799	1304799	type	True	75.0176	178	2467	95	below_threshold
Chondromyces crocatus	strain=Cm c5	GCA_001189295.1	52	52	type	True	75.0171	326	2467	95	below_threshold
Marichromatium purpuratum	strain=984	GCA_000224005.3	37487	37487	type	True	75.0041	155	2467	95	below_threshold
Phycicoccus jejuensis	strain=NRRL B-24460	GCA_000720925.1	367299	367299	type	True	74.9688	298	2467	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	74.9575	389	2467	95	below_threshold
Xanthomonas sacchari	strain=CFBP4641	GCA_002940085.1	56458	56458	suspected-type	True	74.9454	187	2467	95	below_threshold
Phycicoccus mangrovi	strain=KQZ13P-1	GCA_018729305.1	2840470	2840470	type	True	74.9423	309	2467	95	below_threshold
Oharaeibacter diazotrophicus	strain=SM30	GCA_011317485.1	1920512	1920512	type	True	74.9401	274	2467	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	74.9358	386	2467	95	below_threshold
Luteimonas huabeiensis	strain=HB2	GCA_000559025.1	1244513	1244513	type	True	74.9247	246	2467	95	below_threshold
Micromonospora mirobrigensis	strain=DSM 44830	GCA_900091555.1	262898	262898	type	True	74.924	312	2467	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	74.8726	371	2467	95	below_threshold
Micromonospora siamensis	strain=DSM 45097	GCA_900090305.1	299152	299152	type	True	74.8313	317	2467	95	below_threshold
Herbidospora sakaeratensis	strain=NBRC 102641	GCA_001570525.1	564415	564415	type	True	74.8281	360	2467	95	below_threshold
Micromonospora terminaliae	strain=TMS7	GCA_010671825.1	1914461	1914461	type	True	74.8118	332	2467	95	below_threshold
Micromonospora coxensis	strain=DSM 45161	GCA_900090295.1	356852	356852	type	True	74.8109	331	2467	95	below_threshold
Microtetraspora malaysiensis	strain=NBRC 100735	GCA_001528665.1	161358	161358	type	True	74.8053	271	2467	95	below_threshold
Xylophilus rhododendri	strain=KACC 21265	GCA_009906855.1	2697032	2697032	type	True	74.797	178	2467	95	below_threshold
Herbidospora mongoliensis	strain=NBRC 105882	GCA_001570545.1	688067	688067	type	True	74.795	297	2467	95	below_threshold
Micromonospora humi	strain=DSM 45647	GCA_900090105.1	745366	745366	type	True	74.7844	330	2467	95	below_threshold
Herbidospora galbida	strain=NEAU-GS14	GCA_005233835.1	2575442	2575442	type	True	74.7772	333	2467	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 07:30:52,134] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20923/tc_result.tsv
[2023-03-18 07:30:52,134] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:30:52,134] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:30:52,134] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9c4d6b21-0b85-48f7-a6b2-5c11eeac8351/dqc_reference/checkm_data
[2023-03-18 07:30:52,135] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:30:52,267] [INFO] Task started: CheckM
[2023-03-18 07:30:52,267] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20923/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20923/checkm_input OceanDNA-b20923/checkm_result
[2023-03-18 07:32:52,128] [INFO] Task succeeded: CheckM
[2023-03-18 07:32:52,128] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 07:32:52,132] [INFO] ===== Completeness check finished =====
[2023-03-18 07:32:52,133] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:32:52,133] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20923/markers.fasta)
[2023-03-18 07:32:52,133] [INFO] Task started: Blastn
[2023-03-18 07:32:52,133] [INFO] Running command: blastn -query OceanDNA-b20923/markers.fasta -db /var/lib/cwl/stg9c4d6b21-0b85-48f7-a6b2-5c11eeac8351/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20923/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:32:53,529] [INFO] Task succeeded: Blastn
[2023-03-18 07:32:53,530] [INFO] Selected 19 target genomes.
[2023-03-18 07:32:53,530] [INFO] Target genome list was writen to OceanDNA-b20923/target_genomes_gtdb.txt
[2023-03-18 07:32:53,968] [INFO] Task started: fastANI
[2023-03-18 07:32:53,968] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfd6c23f-a239-40b6-8456-fe4d0d200723/OceanDNA-b20923.fa --refList OceanDNA-b20923/target_genomes_gtdb.txt --output OceanDNA-b20923/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:33:15,275] [INFO] Task succeeded: fastANI
[2023-03-18 07:33:15,285] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 07:33:15,285] [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_002320815.1	s__UBA1660 sp002320815	99.9433	2395	2467	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__UBA1660	95.0	99.96	99.96	0.96	0.96	2	conclusive
GCA_017644045.1	s__UBA1660 sp017644045	80.908	1492	2467	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__UBA1660	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002699025.1	s__GCA-2699025 sp002699025	77.8287	1042	2467	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__GCA-2699025	95.0	99.90	99.85	0.97	0.97	3	-
GCA_009992505.1	s__JAADHO01 sp009992505	76.6821	297	2467	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__JAADHO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012744445.1	s__JAAYBZ01 sp012744445	76.6275	387	2467	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__JAAYBZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016706685.1	s__JADJJE01 sp016706685	76.5069	483	2467	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__JADJJE01	95.0	99.15	99.06	0.93	0.90	7	-
GCA_013151775.1	s__JAADHO01 sp013151775	76.3972	417	2467	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__JAADHO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000737325.1	s__Sandaracinus amylolyticus	75.7283	690	2467	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Sandaracinaceae;g__Sandaracinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004283055.1	s__SG8-38 sp004283055	75.6147	136	2467	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__SG8-38	95.0	99.78	99.72	0.93	0.90	8	-
GCA_017881145.1	s__JADGRF01 sp017881145	75.48	124	2467	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__JAFGIB01;g__JADGRF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006226565.1	s__PHBI01 sp006226565	75.3207	513	2467	d__Bacteria;p__Myxococcota;c__UBA9042;o__PHBI01;f__PHBI01;g__PHBI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016214955.1	s__JACRMN01 sp016214955	75.2108	393	2467	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__JACRMN01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343155.1	s__Marichromatium gracile	75.0254	161	2467	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Marichromatium	95.0	98.88	96.74	0.96	0.94	6	-
GCF_000224005.2	s__Marichromatium purpuratum	75.0031	155	2467	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Marichromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795205.1	s__JAEUHZ01 sp016795205	74.9328	234	2467	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JAEUHZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129635.1	s__Singulisphaera sp900129635	74.7946	112	2467	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Singulisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900090105.1	s__Micromonospora humi	74.7713	345	2467	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 07:33:15,285] [INFO] GTDB search result was written to OceanDNA-b20923/result_gtdb.tsv
[2023-03-18 07:33:15,285] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:33:15,288] [INFO] DFAST_QC result json was written to OceanDNA-b20923/dqc_result.json
[2023-03-18 07:33:15,288] [INFO] DFAST_QC completed!
[2023-03-18 07:33:15,288] [INFO] Total running time: 0h3m45s