[2023-03-17 11:00:13,112] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:00:13,113] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:00:13,113] [INFO] DQC Reference Directory: /var/lib/cwl/stg8d070a82-b9be-47e9-b095-cb161f62ebfa/dqc_reference
[2023-03-17 11:00:14,189] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:00:14,189] [INFO] Task started: Prodigal
[2023-03-17 11:00:14,189] [INFO] Running command: cat /var/lib/cwl/stg8aea5231-eb65-406e-a2c0-35f1f35fc2e9/OceanDNA-b2877.fa | prodigal -d OceanDNA-b2877/cds.fna -a OceanDNA-b2877/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:00:33,100] [INFO] Task succeeded: Prodigal
[2023-03-17 11:00:33,100] [INFO] Task started: HMMsearch
[2023-03-17 11:00:33,100] [INFO] Running command: hmmsearch --tblout OceanDNA-b2877/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8d070a82-b9be-47e9-b095-cb161f62ebfa/dqc_reference/reference_markers.hmm OceanDNA-b2877/protein.faa > /dev/null
[2023-03-17 11:00:33,295] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:00:33,295] [INFO] Found 6/6 markers.
[2023-03-17 11:00:33,318] [INFO] Query marker FASTA was written to OceanDNA-b2877/markers.fasta
[2023-03-17 11:00:33,319] [INFO] Task started: Blastn
[2023-03-17 11:00:33,319] [INFO] Running command: blastn -query OceanDNA-b2877/markers.fasta -db /var/lib/cwl/stg8d070a82-b9be-47e9-b095-cb161f62ebfa/dqc_reference/reference_markers.fasta -out OceanDNA-b2877/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:00:34,438] [INFO] Task succeeded: Blastn
[2023-03-17 11:00:34,439] [INFO] Selected 23 target genomes.
[2023-03-17 11:00:34,439] [INFO] Target genome list was writen to OceanDNA-b2877/target_genomes.txt
[2023-03-17 11:00:34,495] [INFO] Task started: fastANI
[2023-03-17 11:00:34,495] [INFO] Running command: fastANI --query /var/lib/cwl/stg8aea5231-eb65-406e-a2c0-35f1f35fc2e9/OceanDNA-b2877.fa --refList OceanDNA-b2877/target_genomes.txt --output OceanDNA-b2877/fastani_result.tsv --threads 1
[2023-03-17 11:00:56,212] [INFO] Task succeeded: fastANI
[2023-03-17 11:00:56,213] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8d070a82-b9be-47e9-b095-cb161f62ebfa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:00:56,213] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8d070a82-b9be-47e9-b095-cb161f62ebfa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:00:56,226] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:00:56,226] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 11:00:56,226] [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
Candidatus Mycolicibacterium alkanivorans		GCA_022760805.1	2954114	2954114	type	True	80.4829	539	1003	95	below_threshold
Mycolicibacterium anyangense	strain=JCM 30275	GCA_010731855.1	1431246	1431246	type	True	79.9639	623	1003	95	below_threshold
Mycolicibacterium fallax	strain=JCM 6405	GCA_010726955.1	1793	1793	type	True	79.6019	497	1003	95	below_threshold
Mycolicibacterium fallax	strain=DSM 44179	GCA_002101995.1	1793	1793	type	True	79.5482	496	1003	95	below_threshold
Mycobacterium palauense	strain=CECT 8779	GCA_002592005.1	2034511	2034511	type	True	79.5292	540	1003	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	79.5117	585	1003	95	below_threshold
Mycolicibacterium rhodesiae	strain=DSM 44223	GCA_002086695.1	36814	36814	type	True	79.4939	585	1003	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.4926	584	1003	95	below_threshold
Mycolicibacterium phlei	strain=DSM 43239 = CCUG 21000	GCA_001582015.1	1771	1771	type	True	79.4791	535	1003	95	below_threshold
Mycolicibacterium aromaticivorans	strain=JS19b1	GCA_000559085.2	318425	318425	type	True	79.4496	563	1003	95	below_threshold
Mycolicibacterium helvum	strain=JCM 30396	GCA_010731895.1	1534349	1534349	type	True	79.3727	556	1003	95	below_threshold
Mycobacterium avium subsp. avium	strain=DSM 44156	GCA_009741445.1	44454	1764	type	True	79.1997	466	1003	95	below_threshold
Mycolicibacterium thermoresistibile	strain=NCTC10409	GCA_900187065.1	1797	1797	type	True	79.1834	475	1003	95	below_threshold
Mycolicibacterium canariasense	strain=JCM15298	GCA_001570445.1	228230	228230	type	True	79.1601	484	1003	95	below_threshold
Mycobacterium avium subsp. avium	strain=ATCC 25291	GCA_000174035.1	44454	1764	type	True	79.1543	452	1003	95	below_threshold
Mycolicibacterium thermoresistibile	strain=JCM6362	GCA_001570505.1	1797	1797	type	True	79.146	477	1003	95	below_threshold
Mycolicibacterium thermoresistibile	strain=ATCC 19527	GCA_000234585.2	1797	1797	type	True	79.1457	474	1003	95	below_threshold
Mycolicibacterium llatzerense	strain=MG13	GCA_025331195.1	280871	280871	type	True	78.8314	440	1003	95	below_threshold
Mycolicibacterium baixiangningiae	strain=LJ126	GCA_016313185.1	2761578	2761578	type	True	78.8022	457	1003	95	below_threshold
Mycolicibacterium baixiangningiae	strain=LJ126	GCA_014893035.1	2761578	2761578	type	True	78.7565	463	1003	95	below_threshold
Mycolicibacterium conceptionense	strain=CCUG 50187	GCA_002102065.1	451644	451644	suspected-type	True	78.6763	465	1003	95	below_threshold
Mycolicibacterium mengxianglii	strain=Z-34	GCA_015710575.2	2736649	2736649	type	True	78.4671	433	1003	95	below_threshold
Mycolicibacter arupensis	strain=DSM 44942	GCA_002086515.1	342002	342002	type	True	78.3038	386	1003	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 11:00:56,231] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2877/tc_result.tsv
[2023-03-17 11:00:56,238] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:00:56,238] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:00:56,238] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8d070a82-b9be-47e9-b095-cb161f62ebfa/dqc_reference/checkm_data
[2023-03-17 11:00:56,239] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:00:56,244] [INFO] Task started: CheckM
[2023-03-17 11:00:56,244] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2877/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2877/checkm_input OceanDNA-b2877/checkm_result
[2023-03-17 11:01:45,050] [INFO] Task succeeded: CheckM
[2023-03-17 11:01:45,051] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.51%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 11:01:45,060] [INFO] ===== Completeness check finished =====
[2023-03-17 11:01:45,060] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:01:45,060] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2877/markers.fasta)
[2023-03-17 11:01:45,061] [INFO] Task started: Blastn
[2023-03-17 11:01:45,061] [INFO] Running command: blastn -query OceanDNA-b2877/markers.fasta -db /var/lib/cwl/stg8d070a82-b9be-47e9-b095-cb161f62ebfa/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2877/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:01:46,917] [INFO] Task succeeded: Blastn
[2023-03-17 11:01:46,918] [INFO] Selected 20 target genomes.
[2023-03-17 11:01:46,918] [INFO] Target genome list was writen to OceanDNA-b2877/target_genomes_gtdb.txt
[2023-03-17 11:01:46,958] [INFO] Task started: fastANI
[2023-03-17 11:01:46,958] [INFO] Running command: fastANI --query /var/lib/cwl/stg8aea5231-eb65-406e-a2c0-35f1f35fc2e9/OceanDNA-b2877.fa --refList OceanDNA-b2877/target_genomes_gtdb.txt --output OceanDNA-b2877/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:02:05,099] [INFO] Task succeeded: fastANI
[2023-03-17 11:02:05,111] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 11:02:05,111] [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_001510415.1	s__Mycobacterium sp001510415	98.0943	498	1003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_005787665.1	s__Mycobacterium sp005787665	81.6394	562	1003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017853185.1	s__Mycobacterium sp017853185	81.1768	619	1003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903884065.1	s__Mycobacterium sp903884065	81.1404	708	1003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.70	99.70	0.92	0.92	2	-
GCA_903877095.1	s__Mycobacterium sp903877095	80.788	665	1003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.96	99.94	0.97	0.96	4	-
GCA_018883075.1	s__Mycobacterium sp018883075	80.5591	492	1003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018500045.1	s__Mycobacterium sp018500045	80.5318	440	1003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903862565.1	s__Mycobacterium sp903862565	80.4036	590	1003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001494595.1	s__Mycobacterium sp001494595	80.1219	638	1003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011694515.1	s__Mycobacterium sp011694515	80.0276	612	1003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731855.1	s__Mycobacterium anyangense	79.9419	625	1003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018882965.1	s__Mycobacterium sp018882965	79.9094	583	1003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401645.1	s__Mycobacterium sp018401645	79.7978	492	1003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008329905.1	s__Mycobacterium sp008329905	79.5003	598	1003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001886515.1	s__Mycobacterium sp001886515	79.4628	602	1003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.54	98.54	0.94	0.94	2	-
GCF_004570325.1	s__Mycobacterium sp004570325	79.2844	506	1003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002101555.1	s__Mycobacterium canariasense	79.2232	475	1003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900187065.1	s__Mycobacterium thermoresistibile	79.1926	475	1003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.97	1.00	1.00	3	-
GCF_018455725.1	s__Mycobacterium sp018455725	79.1162	445	1003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002104795.1	s__Mycobacterium koreense	78.7584	428	1003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.42	98.84	0.96	0.92	3	-
--------------------------------------------------------------------------------
[2023-03-17 11:02:05,111] [INFO] GTDB search result was written to OceanDNA-b2877/result_gtdb.tsv
[2023-03-17 11:02:05,111] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:02:05,113] [INFO] DFAST_QC result json was written to OceanDNA-b2877/dqc_result.json
[2023-03-17 11:02:05,114] [INFO] DFAST_QC completed!
[2023-03-17 11:02:05,114] [INFO] Total running time: 0h1m52s