[2023-06-30 04:32:53,535] [INFO] DFAST_QC pipeline started.
[2023-06-30 04:32:53,540] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 04:32:53,540] [INFO] DQC Reference Directory: /var/lib/cwl/stg6c71c06d-b381-4d8d-a4c9-23eab96f92b0/dqc_reference
[2023-06-30 04:32:55,269] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 04:32:55,270] [INFO] Task started: Prodigal
[2023-06-30 04:32:55,271] [INFO] Running command: gunzip -c /var/lib/cwl/stg433f76fc-79d4-4d8b-80f0-8a7020628e9f/GCA_903879565.1_freshwater_MAG_---_MJ130820A_bin-457_genomic.fna.gz | prodigal -d GCA_903879565.1_freshwater_MAG_---_MJ130820A_bin-457_genomic.fna/cds.fna -a GCA_903879565.1_freshwater_MAG_---_MJ130820A_bin-457_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 04:33:07,144] [INFO] Task succeeded: Prodigal
[2023-06-30 04:33:07,144] [INFO] Task started: HMMsearch
[2023-06-30 04:33:07,145] [INFO] Running command: hmmsearch --tblout GCA_903879565.1_freshwater_MAG_---_MJ130820A_bin-457_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6c71c06d-b381-4d8d-a4c9-23eab96f92b0/dqc_reference/reference_markers.hmm GCA_903879565.1_freshwater_MAG_---_MJ130820A_bin-457_genomic.fna/protein.faa > /dev/null
[2023-06-30 04:33:07,461] [INFO] Task succeeded: HMMsearch
[2023-06-30 04:33:07,463] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg433f76fc-79d4-4d8b-80f0-8a7020628e9f/GCA_903879565.1_freshwater_MAG_---_MJ130820A_bin-457_genomic.fna.gz]
[2023-06-30 04:33:07,510] [INFO] Query marker FASTA was written to GCA_903879565.1_freshwater_MAG_---_MJ130820A_bin-457_genomic.fna/markers.fasta
[2023-06-30 04:33:07,511] [INFO] Task started: Blastn
[2023-06-30 04:33:07,511] [INFO] Running command: blastn -query GCA_903879565.1_freshwater_MAG_---_MJ130820A_bin-457_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c71c06d-b381-4d8d-a4c9-23eab96f92b0/dqc_reference/reference_markers.fasta -out GCA_903879565.1_freshwater_MAG_---_MJ130820A_bin-457_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 04:33:08,491] [INFO] Task succeeded: Blastn
[2023-06-30 04:33:08,496] [INFO] Selected 13 target genomes.
[2023-06-30 04:33:08,496] [INFO] Target genome list was writen to GCA_903879565.1_freshwater_MAG_---_MJ130820A_bin-457_genomic.fna/target_genomes.txt
[2023-06-30 04:33:08,498] [INFO] Task started: fastANI
[2023-06-30 04:33:08,499] [INFO] Running command: fastANI --query /var/lib/cwl/stg433f76fc-79d4-4d8b-80f0-8a7020628e9f/GCA_903879565.1_freshwater_MAG_---_MJ130820A_bin-457_genomic.fna.gz --refList GCA_903879565.1_freshwater_MAG_---_MJ130820A_bin-457_genomic.fna/target_genomes.txt --output GCA_903879565.1_freshwater_MAG_---_MJ130820A_bin-457_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 04:33:22,004] [INFO] Task succeeded: fastANI
[2023-06-30 04:33:22,005] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6c71c06d-b381-4d8d-a4c9-23eab96f92b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 04:33:22,005] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6c71c06d-b381-4d8d-a4c9-23eab96f92b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 04:33:22,017] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2023-06-30 04:33:22,017] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-30 04:33:22,017] [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
Mycolicibacterium fluoranthenivorans	strain=DSM 44556	GCA_011758805.1	258505	258505	type	True	96.066	622	705	95	conclusive
Mycolicibacterium cosmeticum	strain=DSM 44829	GCA_005670675.1	258533	258533	type	True	84.5419	549	705	95	below_threshold
Mycolicibacterium cosmeticum	strain=DSM 44829	GCA_000613185.1	258533	258533	type	True	84.5233	548	705	95	below_threshold
Mycolicibacterium canariasense	strain=CCUG 47953	GCA_002101555.1	228230	228230	type	True	84.4181	517	705	95	below_threshold
Mycolicibacterium canariasense	strain=JCM15298	GCA_001570445.1	228230	228230	type	True	84.3678	521	705	95	below_threshold
Mycolicibacterium bacteremicum	strain=DSM 45578	GCA_002086115.1	564198	564198	type	True	80.9056	421	705	95	below_threshold
Mycolicibacterium boenickei	strain=JCM 15653	GCA_010731295.1	146017	146017	type	True	80.1066	382	705	95	below_threshold
Mycolicibacterium phlei	strain=DSM 43239 = CCUG 21000	GCA_001582015.1	1771	1771	type	True	80.0352	361	705	95	below_threshold
Mycolicibacterium llatzerense	strain=MG13	GCA_025331195.1	280871	280871	type	True	79.7654	326	705	95	below_threshold
Mycolicibacterium fallax	strain=JCM 6405	GCA_010726955.1	1793	1793	type	True	79.6003	278	705	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	79.4345	315	705	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.2424	331	705	95	below_threshold
Mycolicibacterium mengxianglii	strain=Z-34	GCA_015710575.2	2736649	2736649	type	True	79.2197	295	705	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 04:33:22,019] [INFO] DFAST Taxonomy check result was written to GCA_903879565.1_freshwater_MAG_---_MJ130820A_bin-457_genomic.fna/tc_result.tsv
[2023-06-30 04:33:22,020] [INFO] ===== Taxonomy check completed =====
[2023-06-30 04:33:22,020] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 04:33:22,020] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6c71c06d-b381-4d8d-a4c9-23eab96f92b0/dqc_reference/checkm_data
[2023-06-30 04:33:22,021] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 04:33:22,070] [INFO] Task started: CheckM
[2023-06-30 04:33:22,071] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903879565.1_freshwater_MAG_---_MJ130820A_bin-457_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903879565.1_freshwater_MAG_---_MJ130820A_bin-457_genomic.fna/checkm_input GCA_903879565.1_freshwater_MAG_---_MJ130820A_bin-457_genomic.fna/checkm_result
[2023-06-30 04:33:59,043] [INFO] Task succeeded: CheckM
[2023-06-30 04:33:59,044] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.18%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 04:33:59,069] [INFO] ===== Completeness check finished =====
[2023-06-30 04:33:59,070] [INFO] ===== Start GTDB Search =====
[2023-06-30 04:33:59,070] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903879565.1_freshwater_MAG_---_MJ130820A_bin-457_genomic.fna/markers.fasta)
[2023-06-30 04:33:59,071] [INFO] Task started: Blastn
[2023-06-30 04:33:59,071] [INFO] Running command: blastn -query GCA_903879565.1_freshwater_MAG_---_MJ130820A_bin-457_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c71c06d-b381-4d8d-a4c9-23eab96f92b0/dqc_reference/reference_markers_gtdb.fasta -out GCA_903879565.1_freshwater_MAG_---_MJ130820A_bin-457_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 04:34:00,467] [INFO] Task succeeded: Blastn
[2023-06-30 04:34:00,472] [INFO] Selected 15 target genomes.
[2023-06-30 04:34:00,472] [INFO] Target genome list was writen to GCA_903879565.1_freshwater_MAG_---_MJ130820A_bin-457_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 04:34:00,477] [INFO] Task started: fastANI
[2023-06-30 04:34:00,477] [INFO] Running command: fastANI --query /var/lib/cwl/stg433f76fc-79d4-4d8b-80f0-8a7020628e9f/GCA_903879565.1_freshwater_MAG_---_MJ130820A_bin-457_genomic.fna.gz --refList GCA_903879565.1_freshwater_MAG_---_MJ130820A_bin-457_genomic.fna/target_genomes_gtdb.txt --output GCA_903879565.1_freshwater_MAG_---_MJ130820A_bin-457_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 04:34:15,596] [INFO] Task succeeded: fastANI
[2023-06-30 04:34:15,613] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 04:34:15,614] [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_011758805.1	s__Mycobacterium fluoranthenivorans	96.066	622	705	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.15	95.95	0.85	0.84	4	conclusive
GCA_016197365.1	s__Mycobacterium cosmeticum_A	85.7064	494	705	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000613185.1	s__Mycobacterium cosmeticum	84.5628	545	705	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.89	98.33	0.93	0.89	4	-
GCF_002101555.1	s__Mycobacterium canariasense	84.4374	516	705	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900078775.1	s__Mycobacterium aurum_A	81.5222	428	705	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001907655.1	s__Mycobacterium diernhoferi	81.3383	432	705	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.97	99.94	1.00	1.00	3	-
GCF_001644575.1	s__Mycobacterium sp001644575	81.3294	428	705	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.69	99.69	0.98	0.98	2	-
GCF_002086115.1	s__Mycobacterium bacteremicum	80.9061	421	705	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000317305.3	s__Mycobacterium neoaurum_A	80.4801	392	705	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.30	95.79	0.98	0.90	7	-
GCF_004762045.1	s__Mycobacterium sp004762045	80.1144	362	705	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731295.1	s__Mycobacterium boenickei	80.1064	382	705	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.96	1.00	1.00	3	-
GCF_017876775.1	s__Mycobacterium lutetiense	79.7453	355	705	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002102345.1	s__Mycobacterium peregrinum	79.6374	370	705	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.04	98.27	0.94	0.91	5	-
GCF_010729665.1	s__Mycobacterium madagascariense	79.2363	339	705	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002798385.1	s__Mycobacterium goodii	79.2247	354	705	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.16	99.12	0.92	0.89	7	-
--------------------------------------------------------------------------------
[2023-06-30 04:34:15,616] [INFO] GTDB search result was written to GCA_903879565.1_freshwater_MAG_---_MJ130820A_bin-457_genomic.fna/result_gtdb.tsv
[2023-06-30 04:34:15,617] [INFO] ===== GTDB Search completed =====
[2023-06-30 04:34:15,621] [INFO] DFAST_QC result json was written to GCA_903879565.1_freshwater_MAG_---_MJ130820A_bin-457_genomic.fna/dqc_result.json
[2023-06-30 04:34:15,621] [INFO] DFAST_QC completed!
[2023-06-30 04:34:15,621] [INFO] Total running time: 0h1m22s