[2023-03-15 13:39:34,879] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:39:34,881] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:39:34,881] [INFO] DQC Reference Directory: /var/lib/cwl/stgfe9f9597-4c54-46f7-90a2-980facb605e0/dqc_reference
[2023-03-15 13:39:37,045] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:39:37,047] [INFO] Task started: Prodigal
[2023-03-15 13:39:37,047] [INFO] Running command: cat /var/lib/cwl/stg32ad2b1c-8609-4753-96cf-e6e802d1b7ad/OceanDNA-b2591.fa | prodigal -d OceanDNA-b2591/cds.fna -a OceanDNA-b2591/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:39:53,373] [INFO] Task succeeded: Prodigal
[2023-03-15 13:39:53,374] [INFO] Task started: HMMsearch
[2023-03-15 13:39:53,374] [INFO] Running command: hmmsearch --tblout OceanDNA-b2591/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfe9f9597-4c54-46f7-90a2-980facb605e0/dqc_reference/reference_markers.hmm OceanDNA-b2591/protein.faa > /dev/null
[2023-03-15 13:39:53,558] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:39:53,559] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg32ad2b1c-8609-4753-96cf-e6e802d1b7ad/OceanDNA-b2591.fa]
[2023-03-15 13:39:53,582] [INFO] Query marker FASTA was written to OceanDNA-b2591/markers.fasta
[2023-03-15 13:39:53,583] [INFO] Task started: Blastn
[2023-03-15 13:39:53,583] [INFO] Running command: blastn -query OceanDNA-b2591/markers.fasta -db /var/lib/cwl/stgfe9f9597-4c54-46f7-90a2-980facb605e0/dqc_reference/reference_markers.fasta -out OceanDNA-b2591/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:39:54,456] [INFO] Task succeeded: Blastn
[2023-03-15 13:39:54,461] [INFO] Selected 23 target genomes.
[2023-03-15 13:39:54,461] [INFO] Target genome list was writen to OceanDNA-b2591/target_genomes.txt
[2023-03-15 13:39:54,475] [INFO] Task started: fastANI
[2023-03-15 13:39:54,475] [INFO] Running command: fastANI --query /var/lib/cwl/stg32ad2b1c-8609-4753-96cf-e6e802d1b7ad/OceanDNA-b2591.fa --refList OceanDNA-b2591/target_genomes.txt --output OceanDNA-b2591/fastani_result.tsv --threads 1
[2023-03-15 13:40:09,046] [INFO] Task succeeded: fastANI
[2023-03-15 13:40:09,046] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfe9f9597-4c54-46f7-90a2-980facb605e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:40:09,046] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfe9f9597-4c54-46f7-90a2-980facb605e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:40:09,060] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:40:09,061] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 13:40:09,061] [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 ureisolvens	strain=CFH S00084	GCA_015278315.1	2781186	2781186	type	True	79.3479	376	886	95	below_threshold
Microbacterium trichothecenolyticum	strain=DSM 8608	GCA_000956465.1	69370	69370	type	True	79.2611	387	886	95	below_threshold
Microbacterium sulfonylureivorans	strain=LAM7116	GCA_003999995.1	2486854	2486854	type	True	79.214	360	886	95	below_threshold
Microbacterium thalassium	strain=DSM 12511	GCA_014208045.1	362649	362649	type	True	79.1953	361	886	95	below_threshold
Microbacterium kyungheense	strain=DSM 105492	GCA_006783905.1	1263636	1263636	type	True	79.186	357	886	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	79.1718	389	886	95	below_threshold
Microbacterium flavescens	strain=JCM 3877	GCA_018588945.1	69366	69366	type	True	79.1372	372	886	95	below_threshold
Microbacterium cremeum	strain=NY27	GCA_015277855.1	2782169	2782169	type	True	79.1341	387	886	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	79.0717	386	886	95	below_threshold
Microbacterium invictum	strain=JCM 17023	GCA_015278285.1	515415	515415	type	True	78.9008	322	886	95	below_threshold
Microbacterium invictum	strain=DSM 19600	GCA_023155715.1	515415	515415	type	True	78.8942	323	886	95	below_threshold
Microbacterium wangchenii	strain=dk512	GCA_004564355.1	2541726	2541726	type	True	78.8747	345	886	95	below_threshold
Microbacterium rhizomatis	strain=JCM 30598	GCA_008710745.1	1631477	1631477	type	True	78.8232	358	886	95	below_threshold
Microbacterium saccharophilum	strain=NBRC 108778	GCA_007992455.1	1213358	1213358	type	True	78.8218	337	886	95	below_threshold
Microbacterium saccharophilum	strain=K-1	GCA_008017435.1	1213358	1213358	type	True	78.8004	336	886	95	below_threshold
Microbacterium lushaniae	strain=L-031	GCA_008727775.1	2614639	2614639	type	True	78.7615	338	886	95	below_threshold
Microbacterium bovistercoris	strain=NEAU-LLE	GCA_003387575.1	2293570	2293570	type	True	78.41	287	886	95	below_threshold
Microbacterium oxydans	strain=NBRC 15586	GCA_006540085.1	82380	82380	suspected-type	True	78.3837	277	886	95	below_threshold
Microbacterium oxydans	strain=DSM 20578	GCA_008868025.1	82380	82380	suspected-type	True	78.3695	282	886	95	below_threshold
Microbacterium caowuchunii	strain=ST-M6	GCA_008727755.1	2614638	2614638	type	True	78.3425	313	886	95	below_threshold
Microbacterium mangrovi	strain=MUSC 115	GCA_000802305.1	1348253	1348253	type	True	78.337	302	886	95	below_threshold
Microbacterium paraoxydans	strain=DSM 15019	GCA_900105335.1	199592	199592	suspected-type	True	78.2851	289	886	95	below_threshold
Microbacterium paraoxydans	strain=NBRC 103076	GCA_001552495.1	199592	199592	suspected-type	True	78.2084	262	886	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 13:40:09,062] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2591/tc_result.tsv
[2023-03-15 13:40:09,064] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:40:09,064] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:40:09,064] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfe9f9597-4c54-46f7-90a2-980facb605e0/dqc_reference/checkm_data
[2023-03-15 13:40:09,065] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:40:09,087] [INFO] Task started: CheckM
[2023-03-15 13:40:09,087] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2591/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2591/checkm_input OceanDNA-b2591/checkm_result
[2023-03-15 13:40:51,917] [INFO] Task succeeded: CheckM
[2023-03-15 13:40:51,917] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 13:40:52,195] [INFO] ===== Completeness check finished =====
[2023-03-15 13:40:52,195] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:40:52,195] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2591/markers.fasta)
[2023-03-15 13:40:52,195] [INFO] Task started: Blastn
[2023-03-15 13:40:52,195] [INFO] Running command: blastn -query OceanDNA-b2591/markers.fasta -db /var/lib/cwl/stgfe9f9597-4c54-46f7-90a2-980facb605e0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2591/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:40:53,635] [INFO] Task succeeded: Blastn
[2023-03-15 13:40:53,641] [INFO] Selected 11 target genomes.
[2023-03-15 13:40:53,641] [INFO] Target genome list was writen to OceanDNA-b2591/target_genomes_gtdb.txt
[2023-03-15 13:40:53,653] [INFO] Task started: fastANI
[2023-03-15 13:40:53,653] [INFO] Running command: fastANI --query /var/lib/cwl/stg32ad2b1c-8609-4753-96cf-e6e802d1b7ad/OceanDNA-b2591.fa --refList OceanDNA-b2591/target_genomes_gtdb.txt --output OceanDNA-b2591/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:41:01,300] [INFO] Task succeeded: fastANI
[2023-03-15 13:41:01,307] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 13:41:01,307] [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
GCF_002812805.1	s__Microbacterium lacus	97.3072	719	886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	97.80	97.80	0.90	0.90	2	conclusive
GCF_002812725.1	s__Microbacterium sp002812725	85.6799	640	886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.24	99.24	0.94	0.94	2	-
GCA_003476465.1	s__Microbacterium sp003476465	81.8738	245	886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003248605.1	s__Microbacterium sp003248605	80.2138	396	886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001427525.1	s__Microbacterium sp001427525	79.3991	373	886	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	79.3066	361	886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_013409785.1	s__Microbacterium immunditiarum	79.2618	365	886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012524205.1	s__Microbacterium sp012524205	79.1732	358	886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007992455.1	s__Microbacterium saccharophilum	78.8281	336	886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.54	98.03	0.93	0.90	5	-
GCF_000967865.1	s__Microbacterium sp000967865	78.574	301	886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105335.1	s__Microbacterium paraoxydans	78.293	289	886	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.3631	99.12	98.76	0.96	0.92	5	-
--------------------------------------------------------------------------------
[2023-03-15 13:41:01,310] [INFO] GTDB search result was written to OceanDNA-b2591/result_gtdb.tsv
[2023-03-15 13:41:01,312] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:41:01,316] [INFO] DFAST_QC result json was written to OceanDNA-b2591/dqc_result.json
[2023-03-15 13:41:01,316] [INFO] DFAST_QC completed!
[2023-03-15 13:41:01,316] [INFO] Total running time: 0h1m26s