[2023-06-12 23:05:38,387] [INFO] DFAST_QC pipeline started.
[2023-06-12 23:05:38,390] [INFO] DFAST_QC version: 0.5.7
[2023-06-12 23:05:38,391] [INFO] DQC Reference Directory: /var/lib/cwl/stg3388161d-3bff-4e96-95ed-21993a6b105e/dqc_reference
[2023-06-12 23:05:39,770] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-12 23:05:39,771] [INFO] Task started: Prodigal
[2023-06-12 23:05:39,772] [INFO] Running command: gunzip -c /var/lib/cwl/stg9d1ed7fb-5336-401f-b769-3dc869384b2a/GCA_022708865.1_ASM2270886v1_genomic.fna.gz | prodigal -d GCA_022708865.1_ASM2270886v1_genomic.fna/cds.fna -a GCA_022708865.1_ASM2270886v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-12 23:05:51,382] [INFO] Task succeeded: Prodigal
[2023-06-12 23:05:51,383] [INFO] Task started: HMMsearch
[2023-06-12 23:05:51,383] [INFO] Running command: hmmsearch --tblout GCA_022708865.1_ASM2270886v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3388161d-3bff-4e96-95ed-21993a6b105e/dqc_reference/reference_markers.hmm GCA_022708865.1_ASM2270886v1_genomic.fna/protein.faa > /dev/null
[2023-06-12 23:05:51,709] [INFO] Task succeeded: HMMsearch
[2023-06-12 23:05:51,711] [INFO] Found 6/6 markers.
[2023-06-12 23:05:51,751] [INFO] Query marker FASTA was written to GCA_022708865.1_ASM2270886v1_genomic.fna/markers.fasta
[2023-06-12 23:05:51,752] [INFO] Task started: Blastn
[2023-06-12 23:05:51,752] [INFO] Running command: blastn -query GCA_022708865.1_ASM2270886v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3388161d-3bff-4e96-95ed-21993a6b105e/dqc_reference/reference_markers.fasta -out GCA_022708865.1_ASM2270886v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-12 23:05:53,084] [INFO] Task succeeded: Blastn
[2023-06-12 23:05:53,089] [INFO] Selected 30 target genomes.
[2023-06-12 23:05:53,089] [INFO] Target genome list was writen to GCA_022708865.1_ASM2270886v1_genomic.fna/target_genomes.txt
[2023-06-12 23:05:53,100] [INFO] Task started: fastANI
[2023-06-12 23:05:53,100] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d1ed7fb-5336-401f-b769-3dc869384b2a/GCA_022708865.1_ASM2270886v1_genomic.fna.gz --refList GCA_022708865.1_ASM2270886v1_genomic.fna/target_genomes.txt --output GCA_022708865.1_ASM2270886v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-12 23:06:22,191] [INFO] Task succeeded: fastANI
[2023-06-12 23:06:22,192] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3388161d-3bff-4e96-95ed-21993a6b105e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-12 23:06:22,192] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3388161d-3bff-4e96-95ed-21993a6b105e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-12 23:06:22,217] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2023-06-12 23:06:22,217] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-12 23:06:22,218] [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 fallax	strain=JCM 6405	GCA_010726955.1	1793	1793	type	True	80.8169	570	1103	95	below_threshold
Mycolicibacterium chitae	strain=JCM 12403	GCA_010727725.1	1792	1792	type	True	80.8075	657	1103	95	below_threshold
Mycolicibacterium chitae	strain=NCTC10485	GCA_900637205.1	1792	1792	type	True	80.7922	669	1103	95	below_threshold
Mycolicibacterium fallax	strain=DSM 44179	GCA_002101995.1	1793	1793	type	True	80.7232	579	1103	95	below_threshold
Mycobacterium palauense	strain=CECT 8779	GCA_002592005.1	2034511	2034511	type	True	80.5944	640	1103	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_001583415.1	1771	1771	type	True	80.4165	604	1103	95	below_threshold
Mycolicibacterium insubricum	strain=JCM 16366	GCA_010731615.1	444597	444597	type	True	80.3607	562	1103	95	below_threshold
Mycolicibacterium phlei	strain=DSM 43239 = CCUG 21000	GCA_001582015.1	1771	1771	type	True	80.3328	606	1103	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_009192875.1	1771	1771	type	True	80.3062	602	1103	95	below_threshold
Mycolicibacterium chlorophenolicum	strain=NBRC 15527	GCA_001552315.1	37916	37916	type	True	80.2874	620	1103	95	below_threshold
Mycolicibacterium cosmeticum	strain=DSM 44829	GCA_005670675.1	258533	258533	type	True	80.2779	582	1103	95	below_threshold
Mycolicibacterium cosmeticum	strain=DSM 44829	GCA_000613185.1	258533	258533	type	True	80.2366	583	1103	95	below_threshold
Mycolicibacterium chlorophenolicum	strain=DSM 43826	GCA_001044235.1	37916	37916	type	True	80.2326	617	1103	95	below_threshold
Mycolicibacterium rutilum	strain=DSM 45405	GCA_900108565.1	370526	370526	type	True	80.0969	583	1103	95	below_threshold
Candidatus Mycolicibacterium alkanivorans		GCA_022760805.1	2954114	2954114	type	True	79.8754	469	1103	95	below_threshold
Mycolicibacterium tokaiense	strain=NCTC10821	GCA_900453365.1	39695	39695	suspected-type	True	79.8749	560	1103	95	below_threshold
Mycolicibacterium tokaiense	strain=JCM 6373	GCA_010725885.1	39695	39695	suspected-type	True	79.8048	564	1103	95	below_threshold
Mycolicibacterium llatzerense	strain=MG13	GCA_025331195.1	280871	280871	type	True	79.7639	526	1103	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	79.616	574	1103	95	below_threshold
Mycolicibacterium thermoresistibile	strain=NCTC10409	GCA_900187065.1	1797	1797	type	True	79.566	509	1103	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.5645	576	1103	95	below_threshold
Mycolicibacterium thermoresistibile	strain=ATCC 19527	GCA_000234585.2	1797	1797	type	True	79.5199	507	1103	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	79.5115	561	1103	95	below_threshold
Mycolicibacterium thermoresistibile	strain=JCM6362	GCA_001570505.1	1797	1797	type	True	79.5113	505	1103	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=DSM 46621	GCA_000295855.1	144549	1766	type	True	79.4762	558	1103	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	79.4431	612	1103	95	below_threshold
Mycolicibacterium lacusdiani	strain=JXJ CY 35	GCA_021916785.1	2895283	2895283	type	True	79.1978	558	1103	95	below_threshold
Mycolicibacter senuensis	strain=DSM 44999	GCA_002101885.1	386913	386913	type	True	79.1318	475	1103	95	below_threshold
Mycolicibacter senuensis	strain=JCM 16017	GCA_010723225.1	386913	386913	type	True	79.1072	481	1103	95	below_threshold
Mycobacterium arosiense	strain=DSM 45069	GCA_002086125.1	425468	425468	type	True	78.6368	471	1103	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-12 23:06:22,221] [INFO] DFAST Taxonomy check result was written to GCA_022708865.1_ASM2270886v1_genomic.fna/tc_result.tsv
[2023-06-12 23:06:22,222] [INFO] ===== Taxonomy check completed =====
[2023-06-12 23:06:22,222] [INFO] ===== Start completeness check using CheckM =====
[2023-06-12 23:06:22,222] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3388161d-3bff-4e96-95ed-21993a6b105e/dqc_reference/checkm_data
[2023-06-12 23:06:22,224] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-12 23:06:22,273] [INFO] Task started: CheckM
[2023-06-12 23:06:22,274] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022708865.1_ASM2270886v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022708865.1_ASM2270886v1_genomic.fna/checkm_input GCA_022708865.1_ASM2270886v1_genomic.fna/checkm_result
[2023-06-12 23:06:59,317] [INFO] Task succeeded: CheckM
[2023-06-12 23:06:59,318] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.10%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-12 23:06:59,343] [INFO] ===== Completeness check finished =====
[2023-06-12 23:06:59,343] [INFO] ===== Start GTDB Search =====
[2023-06-12 23:06:59,344] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022708865.1_ASM2270886v1_genomic.fna/markers.fasta)
[2023-06-12 23:06:59,344] [INFO] Task started: Blastn
[2023-06-12 23:06:59,344] [INFO] Running command: blastn -query GCA_022708865.1_ASM2270886v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3388161d-3bff-4e96-95ed-21993a6b105e/dqc_reference/reference_markers_gtdb.fasta -out GCA_022708865.1_ASM2270886v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-12 23:07:01,105] [INFO] Task succeeded: Blastn
[2023-06-12 23:07:01,110] [INFO] Selected 31 target genomes.
[2023-06-12 23:07:01,111] [INFO] Target genome list was writen to GCA_022708865.1_ASM2270886v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-12 23:07:01,174] [INFO] Task started: fastANI
[2023-06-12 23:07:01,174] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d1ed7fb-5336-401f-b769-3dc869384b2a/GCA_022708865.1_ASM2270886v1_genomic.fna.gz --refList GCA_022708865.1_ASM2270886v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022708865.1_ASM2270886v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-12 23:07:32,199] [INFO] Task succeeded: fastANI
[2023-06-12 23:07:32,230] [INFO] Found 31 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-12 23:07:32,230] [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_010726955.1	s__Mycobacterium fallax	80.8311	568	1103	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	0.97	0.97	2	-
GCF_900637205.1	s__Mycobacterium chitae	80.804	667	1103	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002592005.1	s__Mycobacterium palauense	80.5866	642	1103	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016197405.1	s__Mycobacterium sp016197405	80.5423	631	1103	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001583415.1	s__Mycobacterium phlei	80.4126	604	1103	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.86	99.38	0.98	0.91	10	-
GCF_010731615.1	s__Mycobacterium insubricum	80.3674	563	1103	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000613185.1	s__Mycobacterium cosmeticum	80.2782	578	1103	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.89	98.33	0.93	0.89	4	-
GCF_001044235.1	s__Mycobacterium chlorophenolicum	80.1876	622	1103	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.8643	98.88	97.93	0.94	0.90	4	-
GCF_001667265.1	s__Mycobacterium sp001667265	80.1654	618	1103	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000612725.1	s__Mycobacterium austroafricanum	80.1329	603	1103	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.53	98.42	0.88	0.88	3	-
GCF_002101555.1	s__Mycobacterium canariasense	79.9596	548	1103	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_004570325.1	s__Mycobacterium sp004570325	79.9318	555	1103	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001545925.1	s__Mycobacterium sp001545925	79.9232	531	1103	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001722335.1	s__Mycobacterium flavescens_A	79.8958	594	1103	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010725885.1	s__Mycobacterium tokaiense	79.8187	563	1103	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.19	96.52	0.94	0.90	4	-
GCF_001500125.1	s__Mycobacterium sp001500125	79.723	573	1103	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001457595.1	s__Mycobacterium smegmatis	79.6841	568	1103	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.88	98.06	0.95	0.91	32	-
GCA_900078375.1	s__Mycobacterium sp900078375	79.555	554	1103	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731895.1	s__Mycobacterium helvum	79.5409	546	1103	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013337765.1	s__Mycobacterium sp003053865	79.5403	580	1103	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	95.43	95.41	0.83	0.83	3	-
GCF_900187065.1	s__Mycobacterium thermoresistibile	79.5316	513	1103	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.97	1.00	1.00	3	-
GCF_011745145.1	s__Mycobacterium sp011745145	79.478	557	1103	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004354905.1	s__Mycobacterium eburneum	79.474	568	1103	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.68	99.68	0.92	0.92	2	-
GCF_017312405.1	s__Mycobacterium sp017312405	79.4413	526	1103	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.98	0.98	0.98	2	-
GCF_018455725.1	s__Mycobacterium sp018455725	79.401	474	1103	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002245535.1	s__Mycobacterium lehmannii	79.369	517	1103	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.2034	97.95	97.72	0.91	0.88	6	-
GCF_005222675.1	s__Mycobacterium sp005222675	79.3346	556	1103	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731875.1	s__Mycobacterium sarraceniae	79.215	515	1103	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010727945.1	s__Mycobacterium cookii	78.7215	462	1103	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086125.1	s__Mycobacterium arosiense	78.6462	470	1103	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	78.0809	271	1103	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-12 23:07:32,232] [INFO] GTDB search result was written to GCA_022708865.1_ASM2270886v1_genomic.fna/result_gtdb.tsv
[2023-06-12 23:07:32,233] [INFO] ===== GTDB Search completed =====
[2023-06-12 23:07:32,239] [INFO] DFAST_QC result json was written to GCA_022708865.1_ASM2270886v1_genomic.fna/dqc_result.json
[2023-06-12 23:07:32,239] [INFO] DFAST_QC completed!
[2023-06-12 23:07:32,239] [INFO] Total running time: 0h1m54s