[2023-03-18 00:56:43,494] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:56:43,494] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:56:43,494] [INFO] DQC Reference Directory: /var/lib/cwl/stg20fc1537-94ca-406d-be1b-e94ffe168eca/dqc_reference
[2023-03-18 00:56:44,581] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:56:44,581] [INFO] Task started: Prodigal
[2023-03-18 00:56:44,581] [INFO] Running command: cat /var/lib/cwl/stgebcdb9ed-5b6b-4bf4-91a5-7b0cba2b6f22/OceanDNA-b2592.fa | prodigal -d OceanDNA-b2592/cds.fna -a OceanDNA-b2592/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:56:57,711] [INFO] Task succeeded: Prodigal
[2023-03-18 00:56:57,711] [INFO] Task started: HMMsearch
[2023-03-18 00:56:57,711] [INFO] Running command: hmmsearch --tblout OceanDNA-b2592/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg20fc1537-94ca-406d-be1b-e94ffe168eca/dqc_reference/reference_markers.hmm OceanDNA-b2592/protein.faa > /dev/null
[2023-03-18 00:56:57,901] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:56:57,901] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgebcdb9ed-5b6b-4bf4-91a5-7b0cba2b6f22/OceanDNA-b2592.fa]
[2023-03-18 00:56:57,921] [INFO] Query marker FASTA was written to OceanDNA-b2592/markers.fasta
[2023-03-18 00:56:57,922] [INFO] Task started: Blastn
[2023-03-18 00:56:57,922] [INFO] Running command: blastn -query OceanDNA-b2592/markers.fasta -db /var/lib/cwl/stg20fc1537-94ca-406d-be1b-e94ffe168eca/dqc_reference/reference_markers.fasta -out OceanDNA-b2592/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:56:58,711] [INFO] Task succeeded: Blastn
[2023-03-18 00:56:58,713] [INFO] Selected 14 target genomes.
[2023-03-18 00:56:58,713] [INFO] Target genome list was writen to OceanDNA-b2592/target_genomes.txt
[2023-03-18 00:56:58,720] [INFO] Task started: fastANI
[2023-03-18 00:56:58,721] [INFO] Running command: fastANI --query /var/lib/cwl/stgebcdb9ed-5b6b-4bf4-91a5-7b0cba2b6f22/OceanDNA-b2592.fa --refList OceanDNA-b2592/target_genomes.txt --output OceanDNA-b2592/fastani_result.tsv --threads 1
[2023-03-18 00:57:07,457] [INFO] Task succeeded: fastANI
[2023-03-18 00:57:07,457] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg20fc1537-94ca-406d-be1b-e94ffe168eca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:57:07,458] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg20fc1537-94ca-406d-be1b-e94ffe168eca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:57:07,467] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 00:57:07,467] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 00:57:07,467] [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 profundi	strain=Shh49	GCA_000763375.1	450380	450380	type	True	98.3721	589	670	95	conclusive
Microbacterium murale	strain=CCM 7640	GCA_014635185.1	1081040	1081040	type	True	90.7708	534	670	95	below_threshold
Microbacterium aerolatum	strain=NBRC 103071	GCA_007988825.1	153731	153731	type	True	82.9112	460	670	95	below_threshold
Microbacterium aerolatum	strain=CCM 4955	GCA_014635005.1	153731	153731	type	True	82.848	473	670	95	below_threshold
Microbacterium ginsengiterrae	strain=JCM 15516	GCA_015278215.1	546115	546115	type	True	81.4287	404	670	95	below_threshold
Microbacterium ginsengiterrae	strain=DSM 24823	GCA_014205075.1	546115	546115	type	True	81.3836	410	670	95	below_threshold
Microbacterium liquefaciens	strain=JCM 3879	GCA_014648755.1	33918	33918	type	True	80.8223	357	670	95	below_threshold
Microbacterium liquefaciens	strain=NBRC 15037	GCA_006539765.1	33918	33918	type	True	80.7572	360	670	95	below_threshold
Microbacterium saperdae	strain=JCM 1352	GCA_014646775.1	69368	69368	type	True	80.4842	382	670	95	below_threshold
Microbacterium bovistercoris	strain=NEAU-LLE	GCA_003387575.1	2293570	2293570	type	True	80.4636	334	670	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	78.7673	274	670	95	below_threshold
Microbacterium oryzae	strain=MB-10	GCA_009735645.1	743009	743009	type	True	78.6972	240	670	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	78.6292	265	670	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	78.3401	274	670	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 00:57:07,468] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2592/tc_result.tsv
[2023-03-18 00:57:07,469] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:57:07,469] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:57:07,469] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg20fc1537-94ca-406d-be1b-e94ffe168eca/dqc_reference/checkm_data
[2023-03-18 00:57:07,470] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:57:07,475] [INFO] Task started: CheckM
[2023-03-18 00:57:07,475] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2592/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2592/checkm_input OceanDNA-b2592/checkm_result
[2023-03-18 00:57:44,023] [INFO] Task succeeded: CheckM
[2023-03-18 00:57:44,024] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 00:57:44,029] [INFO] ===== Completeness check finished =====
[2023-03-18 00:57:44,029] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:57:44,029] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2592/markers.fasta)
[2023-03-18 00:57:44,031] [INFO] Task started: Blastn
[2023-03-18 00:57:44,031] [INFO] Running command: blastn -query OceanDNA-b2592/markers.fasta -db /var/lib/cwl/stg20fc1537-94ca-406d-be1b-e94ffe168eca/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2592/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:57:45,412] [INFO] Task succeeded: Blastn
[2023-03-18 00:57:45,414] [INFO] Selected 15 target genomes.
[2023-03-18 00:57:45,415] [INFO] Target genome list was writen to OceanDNA-b2592/target_genomes_gtdb.txt
[2023-03-18 00:57:45,431] [INFO] Task started: fastANI
[2023-03-18 00:57:45,432] [INFO] Running command: fastANI --query /var/lib/cwl/stgebcdb9ed-5b6b-4bf4-91a5-7b0cba2b6f22/OceanDNA-b2592.fa --refList OceanDNA-b2592/target_genomes_gtdb.txt --output OceanDNA-b2592/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:57:55,329] [INFO] Task succeeded: fastANI
[2023-03-18 00:57:55,339] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 00:57:55,339] [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_000763375.1	s__Microbacterium profundi	98.3483	589	670	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.00	98.00	0.85	0.85	2	conclusive
GCF_014635185.1	s__Microbacterium murale	90.7602	534	670	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007988825.1	s__Microbacterium aerolatum	82.9289	459	670	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_015277895.1	s__Microbacterium sp015277895	82.4981	447	670	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903645325.1	s__Microbacterium sp903645325	82.4346	394	670	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205075.1	s__Microbacterium ginsengiterrae	81.3668	411	670	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.21	98.43	0.95	0.89	3	-
GCF_000685355.1	s__Microbacterium sp000685355	80.9224	401	670	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008868125.1	s__Microbacterium maritypicum	80.7651	373	670	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	97.89	96.90	0.89	0.86	8	-
GCF_002872075.1	s__Microbacterium kitamiense	80.7316	367	670	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000956525.1	s__Microbacterium oxydans_A	80.6957	388	670	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002979655.1	s__Microbacterium sp002979655	80.6047	370	670	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	97.69	97.67	0.91	0.90	5	-
GCF_006716345.1	s__Microbacterium saperdae	80.5399	377	670	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017744855.1	s__Microbacterium sp017744855	80.2285	297	670	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007954505.1	s__Microbacterium sp000800925	80.0556	381	670	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.26	97.84	0.89	0.86	5	-
GCA_003524435.1	s__Microbacterium sp003524435	79.5156	297	670	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 00:57:55,340] [INFO] GTDB search result was written to OceanDNA-b2592/result_gtdb.tsv
[2023-03-18 00:57:55,340] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:57:55,343] [INFO] DFAST_QC result json was written to OceanDNA-b2592/dqc_result.json
[2023-03-18 00:57:55,343] [INFO] DFAST_QC completed!
[2023-03-18 00:57:55,343] [INFO] Total running time: 0h1m12s