[2023-03-15 13:20:53,586] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:20:53,587] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:20:53,587] [INFO] DQC Reference Directory: /var/lib/cwl/stg2a24f8c8-7ea3-462b-b0db-fe8e2774cdd6/dqc_reference
[2023-03-15 13:20:54,799] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:20:54,799] [INFO] Task started: Prodigal
[2023-03-15 13:20:54,799] [INFO] Running command: cat /var/lib/cwl/stgd6e82f21-2677-4f89-89af-3207f2219bf4/OceanDNA-b2923.fa | prodigal -d OceanDNA-b2923/cds.fna -a OceanDNA-b2923/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:21:06,393] [INFO] Task succeeded: Prodigal
[2023-03-15 13:21:06,393] [INFO] Task started: HMMsearch
[2023-03-15 13:21:06,393] [INFO] Running command: hmmsearch --tblout OceanDNA-b2923/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2a24f8c8-7ea3-462b-b0db-fe8e2774cdd6/dqc_reference/reference_markers.hmm OceanDNA-b2923/protein.faa > /dev/null
[2023-03-15 13:21:06,610] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:21:06,611] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd6e82f21-2677-4f89-89af-3207f2219bf4/OceanDNA-b2923.fa]
[2023-03-15 13:21:06,628] [INFO] Query marker FASTA was written to OceanDNA-b2923/markers.fasta
[2023-03-15 13:21:06,630] [INFO] Task started: Blastn
[2023-03-15 13:21:06,630] [INFO] Running command: blastn -query OceanDNA-b2923/markers.fasta -db /var/lib/cwl/stg2a24f8c8-7ea3-462b-b0db-fe8e2774cdd6/dqc_reference/reference_markers.fasta -out OceanDNA-b2923/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:21:07,642] [INFO] Task succeeded: Blastn
[2023-03-15 13:21:07,644] [INFO] Selected 30 target genomes.
[2023-03-15 13:21:07,644] [INFO] Target genome list was writen to OceanDNA-b2923/target_genomes.txt
[2023-03-15 13:21:07,669] [INFO] Task started: fastANI
[2023-03-15 13:21:07,669] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6e82f21-2677-4f89-89af-3207f2219bf4/OceanDNA-b2923.fa --refList OceanDNA-b2923/target_genomes.txt --output OceanDNA-b2923/fastani_result.tsv --threads 1
[2023-03-15 13:21:34,769] [INFO] Task succeeded: fastANI
[2023-03-15 13:21:34,770] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2a24f8c8-7ea3-462b-b0db-fe8e2774cdd6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:21:34,770] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2a24f8c8-7ea3-462b-b0db-fe8e2774cdd6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:21:34,787] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:21:34,787] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 13:21:34,787] [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
Kineococcus vitellinus	strain=T13	GCA_009906315.1	2696565	2696565	type	True	77.2186	109	610	95	below_threshold
Kineococcus rubinsiae	strain=B12	GCA_011839805.1	2609562	2609562	type	True	77.102	107	610	95	below_threshold
Nocardioides jishulii	strain=dk3136	GCA_006007965.1	2575440	2575440	type	True	77.0845	102	610	95	below_threshold
Kineococcus siccus	strain=R8	GCA_009906795.1	2696567	2696567	type	True	77.0637	105	610	95	below_threshold
Nocardioides eburneiflavus	strain=MMS17-SY213	GCA_004785795.1	2518372	2518372	type	True	77.0005	120	610	95	below_threshold
Nocardioides marinus	strain=DSM 18248	GCA_013408145.1	374514	374514	type	True	76.9522	125	610	95	below_threshold
Motilibacter peucedani	strain=RP-AC37	GCA_003634695.1	598650	598650	type	True	76.937	145	610	95	below_threshold
Nonomuraea muscovyensis	strain=DSM 45913	GCA_014207745.1	1124761	1124761	type	True	76.8564	130	610	95	below_threshold
Nonomuraea cavernae	strain=CGMCC 4.7368	GCA_014646355.1	2045107	2045107	type	True	76.8176	110	610	95	below_threshold
Nonomuraea cavernae	strain=SYSU K10005	GCA_020215905.1	2045107	2045107	type	True	76.7948	110	610	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_900101465.1	1045774	1045774	type	True	76.7861	124	610	95	below_threshold
Isoptericola jiangsuensis	strain=DSM 21863	GCA_002563715.1	548579	548579	type	True	76.7389	80	610	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_013409225.1	1045774	1045774	type	True	76.7314	127	610	95	below_threshold
Streptomyces minutiscleroticus	strain=JCM 4790	GCA_014650875.1	68238	68238	type	True	76.6806	126	610	95	below_threshold
Nonomuraea coxensis	strain=DSM 45129	GCA_019397265.1	404386	404386	type	True	76.6363	130	610	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	76.6023	116	610	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	76.574	139	610	95	below_threshold
Jiangella rhizosphaerae	strain=NEAU-YY265	GCA_003579925.1	2293569	2293569	type	True	76.5464	121	610	95	below_threshold
Actinomadura hibisca	strain=NBRC 15177	GCA_001552635.1	68565	68565	type	True	76.4264	121	610	95	below_threshold
Actinomadura atramentaria	strain=SF2197	GCA_000381885.1	1990	1990	type	True	76.4252	113	610	95	below_threshold
Actinomadura roseirufa		GCA_900659635.1	2094049	2094049	type	True	76.3954	105	610	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	76.3564	99	610	95	below_threshold
Streptomyces sulfonofaciens	strain=JCM 5069	GCA_014656295.1	68272	68272	type	True	76.3242	118	610	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	76.3139	99	610	95	below_threshold
Actinomycetospora succinea	strain=DSM 45775	GCA_004363095.1	663603	663603	type	True	76.2961	134	610	95	below_threshold
Actinomadura flavalba	strain=DSM 45200	GCA_000374305.1	1120938	1120938	type	True	76.2887	115	610	95	below_threshold
Planotetraspora silvatica	strain=NBRC 100141	GCA_016863315.1	234614	234614	type	True	76.2711	121	610	95	below_threshold
Streptosporangium amethystogenes	strain=NRRL B-2639	GCA_000721075.1	2002	2002	type	True	76.2289	120	610	95	below_threshold
Agromyces flavus	strain=CPCC 202695	GCA_004366335.2	589382	589382	type	True	76.0943	95	610	95	below_threshold
Agromyces ramosus	strain=DSM 43045	GCA_004216665.1	33879	33879	type	True	76.0564	88	610	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 13:21:34,788] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2923/tc_result.tsv
[2023-03-15 13:21:34,788] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:21:34,788] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:21:34,788] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2a24f8c8-7ea3-462b-b0db-fe8e2774cdd6/dqc_reference/checkm_data
[2023-03-15 13:21:34,789] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:21:34,793] [INFO] Task started: CheckM
[2023-03-15 13:21:34,793] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2923/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2923/checkm_input OceanDNA-b2923/checkm_result
[2023-03-15 13:22:06,889] [INFO] Task succeeded: CheckM
[2023-03-15 13:22:06,889] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 13:22:06,892] [INFO] ===== Completeness check finished =====
[2023-03-15 13:22:06,892] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:22:06,892] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2923/markers.fasta)
[2023-03-15 13:22:06,893] [INFO] Task started: Blastn
[2023-03-15 13:22:06,893] [INFO] Running command: blastn -query OceanDNA-b2923/markers.fasta -db /var/lib/cwl/stg2a24f8c8-7ea3-462b-b0db-fe8e2774cdd6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2923/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:22:08,340] [INFO] Task succeeded: Blastn
[2023-03-15 13:22:08,341] [INFO] Selected 12 target genomes.
[2023-03-15 13:22:08,341] [INFO] Target genome list was writen to OceanDNA-b2923/target_genomes_gtdb.txt
[2023-03-15 13:22:08,351] [INFO] Task started: fastANI
[2023-03-15 13:22:08,351] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6e82f21-2677-4f89-89af-3207f2219bf4/OceanDNA-b2923.fa --refList OceanDNA-b2923/target_genomes_gtdb.txt --output OceanDNA-b2923/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:22:15,184] [INFO] Task succeeded: fastANI
[2023-03-15 13:22:15,191] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 13:22:15,192] [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_903954205.1	s__Mxb001 sp903954205	88.6641	359	610	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__Mxb001	95.0	98.46	98.20	0.79	0.70	14	-
GCA_016870425.1	s__Mxb001 sp016870425	81.6668	392	610	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__Mxb001	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004379115.1	s__Mxb001 sp004379115	80.0215	307	610	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__Mxb001	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016870515.1	s__Mxb001 sp016870515	79.6155	312	610	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__Mxb001	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903848435.1	s__Mxb001 sp903848435	79.6083	235	610	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__Mxb001	95.0	96.93	95.89	0.80	0.74	3	-
GCA_903909555.1	s__Mxb001 sp903909555	79.4699	301	610	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__Mxb001	95.0	99.15	99.05	0.83	0.81	4	-
GCA_017856385.1	s__UBA10649 sp017856385	77.9999	158	610	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA10649	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016717115.1	s__UBA10649 sp016717115	77.8005	182	610	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA10649	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013201035.1	s__Phycicoccus sp013201035	77.2349	138	610	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011299595.1	s__Marmoricola_A sp011299595	77.008	118	610	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018388465.1	s__Cellulomonas sp018388465	76.5878	93	610	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.65	99.29	0.98	0.97	3	-
GCF_014395785.1	s__Nocardioides_B mesophilus	76.5222	130	610	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 13:22:15,192] [INFO] GTDB search result was written to OceanDNA-b2923/result_gtdb.tsv
[2023-03-15 13:22:15,192] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:22:15,195] [INFO] DFAST_QC result json was written to OceanDNA-b2923/dqc_result.json
[2023-03-15 13:22:15,195] [INFO] DFAST_QC completed!
[2023-03-15 13:22:15,195] [INFO] Total running time: 0h1m22s