[2023-03-15 07:52:40,327] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:52:40,327] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:52:40,327] [INFO] DQC Reference Directory: /var/lib/cwl/stgbc5463ad-8271-4218-8f51-e35db76059c9/dqc_reference
[2023-03-15 07:52:41,596] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:52:41,596] [INFO] Task started: Prodigal
[2023-03-15 07:52:41,596] [INFO] Running command: cat /var/lib/cwl/stgeb5e09a8-a87b-426d-97dd-8f0978059e87/OceanDNA-b2585.fa | prodigal -d OceanDNA-b2585/cds.fna -a OceanDNA-b2585/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:52:55,304] [INFO] Task succeeded: Prodigal
[2023-03-15 07:52:55,304] [INFO] Task started: HMMsearch
[2023-03-15 07:52:55,304] [INFO] Running command: hmmsearch --tblout OceanDNA-b2585/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbc5463ad-8271-4218-8f51-e35db76059c9/dqc_reference/reference_markers.hmm OceanDNA-b2585/protein.faa > /dev/null
[2023-03-15 07:52:55,603] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:52:55,603] [INFO] Found 6/6 markers.
[2023-03-15 07:52:55,622] [INFO] Query marker FASTA was written to OceanDNA-b2585/markers.fasta
[2023-03-15 07:52:55,623] [INFO] Task started: Blastn
[2023-03-15 07:52:55,623] [INFO] Running command: blastn -query OceanDNA-b2585/markers.fasta -db /var/lib/cwl/stgbc5463ad-8271-4218-8f51-e35db76059c9/dqc_reference/reference_markers.fasta -out OceanDNA-b2585/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:52:56,859] [INFO] Task succeeded: Blastn
[2023-03-15 07:52:56,860] [INFO] Selected 25 target genomes.
[2023-03-15 07:52:56,860] [INFO] Target genome list was writen to OceanDNA-b2585/target_genomes.txt
[2023-03-15 07:52:56,876] [INFO] Task started: fastANI
[2023-03-15 07:52:56,876] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb5e09a8-a87b-426d-97dd-8f0978059e87/OceanDNA-b2585.fa --refList OceanDNA-b2585/target_genomes.txt --output OceanDNA-b2585/fastani_result.tsv --threads 1
[2023-03-15 07:53:15,176] [INFO] Task succeeded: fastANI
[2023-03-15 07:53:15,176] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbc5463ad-8271-4218-8f51-e35db76059c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:53:15,176] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbc5463ad-8271-4218-8f51-e35db76059c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:53:15,190] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:53:15,190] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 07:53:15,190] [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
Microbacterium ginsengisoli	strain=DSM 18659	GCA_000956535.1	400772	400772	type	True	81.1061	324	730	95	below_threshold
Microbacterium cremeum	strain=NY27	GCA_015277855.1	2782169	2782169	type	True	80.9632	364	730	95	below_threshold
Microbacterium hibisci	strain=CCTCC AB 2016180	GCA_015278255.1	2036000	2036000	type	True	80.8545	370	730	95	below_threshold
Microbacterium kyungheense	strain=DSM 105492	GCA_006783905.1	1263636	1263636	type	True	80.788	345	730	95	below_threshold
Microbacterium thalassium	strain=DSM 12511	GCA_014208045.1	362649	362649	type	True	80.7736	398	730	95	below_threshold
Microbacterium lemovicicum	strain=Viu22	GCA_003991875.1	1072463	1072463	type	True	80.7119	369	730	95	below_threshold
Microbacterium lacticum	strain=DSM 20427	GCA_006716815.1	33885	33885	type	True	80.6841	358	730	95	below_threshold
Microbacterium immunditiarum	strain=DSM 24662	GCA_013409785.1	337480	337480	type	True	80.6663	377	730	95	below_threshold
Microbacterium trichothecenolyticum	strain=DSM 8608	GCA_000956465.1	69370	69370	type	True	80.6562	369	730	95	below_threshold
Microbacterium flavescens	strain=JCM 3877	GCA_018588945.1	69366	69366	type	True	80.6539	363	730	95	below_threshold
Microbacterium imperiale	strain=DSM 20530	GCA_017876655.1	33884	33884	type	True	80.593	345	730	95	below_threshold
Microbacterium telephonicum	strain=S2T63	GCA_003651225.1	1714841	1714841	type	True	80.5844	375	730	95	below_threshold
Microbacterium lacticum	strain=NBRC 14135	GCA_006539445.1	33885	33885	type	True	80.5456	358	730	95	below_threshold
Microbacterium lacticum	strain=JCM 1379	GCA_014646835.1	33885	33885	type	True	80.5374	355	730	95	below_threshold
Microbacterium pullorum	strain=Sa4CUA7	GCA_014836535.1	2762236	2762236	type	True	80.5108	360	730	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	80.4946	381	730	95	below_threshold
Microbacterium wangchenii	strain=dk512	GCA_004564355.1	2541726	2541726	type	True	80.4809	358	730	95	below_threshold
Microbacterium ulmi	strain=JCM 14282	GCA_013004565.1	179095	179095	type	True	80.4609	363	730	95	below_threshold
Microbacterium ulmi	strain=CECT 5976	GCA_011759705.1	179095	179095	type	True	80.4427	370	730	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	80.2734	358	730	95	below_threshold
Microbacterium timonense	strain=Marseille-P5731	GCA_900292075.1	2086576	2086576	type	True	80.2115	362	730	95	below_threshold
Microbacterium rhizomatis	strain=JCM 30598	GCA_008710745.1	1631477	1631477	type	True	79.9643	342	730	95	below_threshold
Microbacterium marinilacus	strain=YM11-607	GCA_019753765.1	415209	415209	type	True	79.6962	351	730	95	below_threshold
Agromyces flavus	strain=CPCC 202695	GCA_004366335.2	589382	589382	type	True	79.1433	281	730	95	below_threshold
Curtobacterium allii	strain=20TX0166	GCA_021271025.1	2878384	2878384	type	True	78.3237	211	730	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 07:53:15,191] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2585/tc_result.tsv
[2023-03-15 07:53:15,191] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:53:15,191] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:53:15,191] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbc5463ad-8271-4218-8f51-e35db76059c9/dqc_reference/checkm_data
[2023-03-15 07:53:15,192] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:53:15,196] [INFO] Task started: CheckM
[2023-03-15 07:53:15,196] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2585/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2585/checkm_input OceanDNA-b2585/checkm_result
[2023-03-15 07:53:51,991] [INFO] Task succeeded: CheckM
[2023-03-15 07:53:51,992] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 07:53:51,994] [INFO] ===== Completeness check finished =====
[2023-03-15 07:53:51,994] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:53:51,994] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2585/markers.fasta)
[2023-03-15 07:53:51,995] [INFO] Task started: Blastn
[2023-03-15 07:53:51,995] [INFO] Running command: blastn -query OceanDNA-b2585/markers.fasta -db /var/lib/cwl/stgbc5463ad-8271-4218-8f51-e35db76059c9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2585/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:53:54,073] [INFO] Task succeeded: Blastn
[2023-03-15 07:53:54,074] [INFO] Selected 25 target genomes.
[2023-03-15 07:53:54,074] [INFO] Target genome list was writen to OceanDNA-b2585/target_genomes_gtdb.txt
[2023-03-15 07:53:54,098] [INFO] Task started: fastANI
[2023-03-15 07:53:54,098] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb5e09a8-a87b-426d-97dd-8f0978059e87/OceanDNA-b2585.fa --refList OceanDNA-b2585/target_genomes_gtdb.txt --output OceanDNA-b2585/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:54:10,450] [INFO] Task succeeded: fastANI
[2023-03-15 07:54:10,464] [INFO] Found 25 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 07:54:10,465] [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_003248605.1	s__Microbacterium sp003248605	82.8026	445	730	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002812725.1	s__Microbacterium sp002812725	81.7629	427	730	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.24	99.24	0.94	0.94	2	-
GCF_002812805.1	s__Microbacterium lacus	81.5971	394	730	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	97.80	97.80	0.90	0.90	2	-
GCF_000956535.1	s__Microbacterium ginsengisoli	81.0724	327	730	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.60	98.14	0.85	0.83	9	-
GCF_011046485.1	s__Microbacterium sp011046485	80.8536	362	730	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014208045.1	s__Microbacterium thalassium	80.7993	396	730	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873155.1	s__Microbacterium sp014873155	80.7821	386	730	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900078385.1	s__Microbacterium sp900078385	80.7599	337	730	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001422925.1	s__Microbacterium sp001422925	80.721	387	730	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003991875.1	s__Microbacterium lemovicicum	80.7107	368	730	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001984105.1	s__Microbacterium sp001984105	80.6623	351	730	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.34	96.71	0.91	0.85	3	-
GCF_013409785.1	s__Microbacterium immunditiarum	80.6503	378	730	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715675.1	s__Microbacterium sp006715675	80.6396	376	730	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018588945.1	s__Microbacterium flavescens	80.6234	364	730	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017831975.1	s__Microbacterium terrae	80.5262	361	730	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003339645.1	s__Microbacterium arborescens	80.4653	326	730	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.05	98.95	0.97	0.96	7	-
GCF_004362195.1	s__Microbacterium sp004362195	80.4419	377	730	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002245215.1	s__Microbacterium sp002245215	80.4396	335	730	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011759705.1	s__Microbacterium ulmi	80.4162	372	730	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900292075.1	s__Microbacterium timonense	80.2435	360	730	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715565.1	s__Microbacterium sp006715565	80.2186	344	730	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102175.1	s__Microbacterium sp900102175	80.0334	352	730	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008710745.1	s__Microbacterium rhizomatis	79.9803	341	730	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003850245.1	s__Microbacterium sp003850245	79.8483	332	730	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007988785.1	s__Agrococcus baldri_A	78.0767	237	730	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agrococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 07:54:10,465] [INFO] GTDB search result was written to OceanDNA-b2585/result_gtdb.tsv
[2023-03-15 07:54:10,465] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:54:10,467] [INFO] DFAST_QC result json was written to OceanDNA-b2585/dqc_result.json
[2023-03-15 07:54:10,467] [INFO] DFAST_QC completed!
[2023-03-15 07:54:10,468] [INFO] Total running time: 0h1m30s