[2023-06-04 18:26:16,657] [INFO] DFAST_QC pipeline started.
[2023-06-04 18:26:16,666] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 18:26:16,667] [INFO] DQC Reference Directory: /var/lib/cwl/stgf04c3f13-d5b0-4f1d-92cc-8fdfa8a74775/dqc_reference
[2023-06-04 18:26:19,527] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 18:26:19,528] [INFO] Task started: Prodigal
[2023-06-04 18:26:19,529] [INFO] Running command: gunzip -c /var/lib/cwl/stg42143281-b90a-4b02-b1a0-c1514147c744/GCA_902754765.1_P1994_120_bin172_mag_fasta_genomic.fna.gz | prodigal -d GCA_902754765.1_P1994_120_bin172_mag_fasta_genomic.fna/cds.fna -a GCA_902754765.1_P1994_120_bin172_mag_fasta_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 18:26:31,973] [INFO] Task succeeded: Prodigal
[2023-06-04 18:26:31,974] [INFO] Task started: HMMsearch
[2023-06-04 18:26:31,974] [INFO] Running command: hmmsearch --tblout GCA_902754765.1_P1994_120_bin172_mag_fasta_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf04c3f13-d5b0-4f1d-92cc-8fdfa8a74775/dqc_reference/reference_markers.hmm GCA_902754765.1_P1994_120_bin172_mag_fasta_genomic.fna/protein.faa > /dev/null
[2023-06-04 18:26:32,255] [INFO] Task succeeded: HMMsearch
[2023-06-04 18:26:32,256] [INFO] Found 6/6 markers.
[2023-06-04 18:26:32,297] [INFO] Query marker FASTA was written to GCA_902754765.1_P1994_120_bin172_mag_fasta_genomic.fna/markers.fasta
[2023-06-04 18:26:32,297] [INFO] Task started: Blastn
[2023-06-04 18:26:32,297] [INFO] Running command: blastn -query GCA_902754765.1_P1994_120_bin172_mag_fasta_genomic.fna/markers.fasta -db /var/lib/cwl/stgf04c3f13-d5b0-4f1d-92cc-8fdfa8a74775/dqc_reference/reference_markers.fasta -out GCA_902754765.1_P1994_120_bin172_mag_fasta_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 18:26:33,296] [INFO] Task succeeded: Blastn
[2023-06-04 18:26:33,301] [INFO] Selected 30 target genomes.
[2023-06-04 18:26:33,302] [INFO] Target genome list was writen to GCA_902754765.1_P1994_120_bin172_mag_fasta_genomic.fna/target_genomes.txt
[2023-06-04 18:26:33,597] [INFO] Task started: fastANI
[2023-06-04 18:26:33,598] [INFO] Running command: fastANI --query /var/lib/cwl/stg42143281-b90a-4b02-b1a0-c1514147c744/GCA_902754765.1_P1994_120_bin172_mag_fasta_genomic.fna.gz --refList GCA_902754765.1_P1994_120_bin172_mag_fasta_genomic.fna/target_genomes.txt --output GCA_902754765.1_P1994_120_bin172_mag_fasta_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 18:27:02,938] [INFO] Task succeeded: fastANI
[2023-06-04 18:27:02,938] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf04c3f13-d5b0-4f1d-92cc-8fdfa8a74775/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 18:27:02,938] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf04c3f13-d5b0-4f1d-92cc-8fdfa8a74775/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 18:27:02,966] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 18:27:02,966] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-04 18:27:02,967] [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 vaccae	strain=NBRC 14118	GCA_001552715.1	1810	1810	type	True	80.1065	670	1266	95	below_threshold
Mycolicibacterium vaccae	strain=95051	GCA_001655245.1	1810	1810	type	True	80.0942	719	1266	95	below_threshold
Mycolicibacterium psychrotolerans	strain=JCM 13323	GCA_010729305.1	216929	216929	type	True	80.08	710	1266	95	below_threshold
Mycolicibacterium chlorophenolicum	strain=DSM 43826	GCA_001044235.1	37916	37916	type	True	79.9941	712	1266	95	below_threshold
Mycolicibacterium chubuense	strain=DSM 44219	GCA_001044255.1	1800	1800	type	True	79.98	703	1266	95	below_threshold
Mycolicibacterium chubuense	strain=DSM 44219	GCA_002086595.1	1800	1800	type	True	79.9569	721	1266	95	below_threshold
Mycolicibacterium chubuense	strain=NCTC10819	GCA_900453455.1	1800	1800	type	True	79.9536	732	1266	95	below_threshold
Mycolicibacterium chlorophenolicum	strain=NBRC 15527	GCA_001552315.1	37916	37916	type	True	79.9236	727	1266	95	below_threshold
Mycolicibacterium aurum	strain=NCTC10437	GCA_900637195.1	1791	1791	type	True	79.8994	711	1266	95	below_threshold
Mycolicibacterium phlei	strain=DSM 43239 = CCUG 21000	GCA_001582015.1	1771	1771	type	True	79.4833	604	1266	95	below_threshold
Mycolicibacterium rutilum	strain=DSM 45405	GCA_900108565.1	370526	370526	type	True	79.3922	639	1266	95	below_threshold
Mycolicibacterium chitae	strain=JCM 12403	GCA_010727725.1	1792	1792	type	True	79.0484	538	1266	95	below_threshold
Mycolicibacterium baixiangningiae	strain=LJ126	GCA_014893035.1	2761578	2761578	type	True	79.0157	556	1266	95	below_threshold
Mycobacterium lehmannii	strain=CECT 8763	GCA_002245535.1	2048550	2048550	type	True	78.9472	545	1266	95	below_threshold
Mycolicibacterium chitae	strain=NCTC10485	GCA_900637205.1	1792	1792	type	True	78.9387	552	1266	95	below_threshold
Mycolicibacterium septicum	strain=type strain: DSM 44393	GCA_000455325.1	98668	98668	type	True	78.9058	561	1266	95	below_threshold
Mycolicibacterium septicum	strain=ATCC 700731	GCA_012396425.1	98668	98668	type	True	78.8511	569	1266	95	below_threshold
Mycolicibacterium canariasense	strain=CCUG 47953	GCA_002101555.1	228230	228230	type	True	78.8137	514	1266	95	below_threshold
Mycolicibacterium canariasense	strain=JCM15298	GCA_001570445.1	228230	228230	type	True	78.8068	514	1266	95	below_threshold
Candidatus Mycolicibacterium alkanivorans		GCA_022760805.1	2954114	2954114	type	True	78.7621	425	1266	95	below_threshold
Mycolicibacterium arabiense	strain=JCM 18538	GCA_010731815.2	1286181	1286181	type	True	78.7399	555	1266	95	below_threshold
Mycolicibacterium lacusdiani	strain=JXJ CY 35	GCA_021916785.1	2895283	2895283	type	True	78.6843	562	1266	95	below_threshold
Mycolicibacterium mageritense	strain=CIP 104973	GCA_000612825.1	53462	53462	type	True	78.6233	537	1266	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	78.5884	481	1266	95	below_threshold
Mycolicibacterium mageritense	strain=JCM 12375	GCA_010727475.1	53462	53462	type	True	78.5792	538	1266	95	below_threshold
Mycolicibacterium mengxianglii	strain=Z-34	GCA_015710575.2	2736649	2736649	type	True	78.541	454	1266	95	below_threshold
Mycolicibacterium thermoresistibile	strain=NCTC10409	GCA_900187065.1	1797	1797	type	True	78.4787	496	1266	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	78.4306	504	1266	95	below_threshold
Mycobacterium nebraskense	strain=DSM 44803	GCA_002102255.1	244292	244292	type	True	78.1644	413	1266	95	below_threshold
Mycobacterium paraseoulense	strain=JCM 16952	GCA_010731655.1	590652	590652	type	True	78.1517	432	1266	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 18:27:02,969] [INFO] DFAST Taxonomy check result was written to GCA_902754765.1_P1994_120_bin172_mag_fasta_genomic.fna/tc_result.tsv
[2023-06-04 18:27:02,969] [INFO] ===== Taxonomy check completed =====
[2023-06-04 18:27:02,969] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 18:27:02,970] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf04c3f13-d5b0-4f1d-92cc-8fdfa8a74775/dqc_reference/checkm_data
[2023-06-04 18:27:02,971] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 18:27:03,019] [INFO] Task started: CheckM
[2023-06-04 18:27:03,020] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902754765.1_P1994_120_bin172_mag_fasta_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902754765.1_P1994_120_bin172_mag_fasta_genomic.fna/checkm_input GCA_902754765.1_P1994_120_bin172_mag_fasta_genomic.fna/checkm_result
[2023-06-04 18:27:41,579] [INFO] Task succeeded: CheckM
[2023-06-04 18:27:41,585] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.24%
Contamintation: 2.55%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-04 18:27:41,612] [INFO] ===== Completeness check finished =====
[2023-06-04 18:27:41,613] [INFO] ===== Start GTDB Search =====
[2023-06-04 18:27:41,613] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902754765.1_P1994_120_bin172_mag_fasta_genomic.fna/markers.fasta)
[2023-06-04 18:27:41,614] [INFO] Task started: Blastn
[2023-06-04 18:27:41,614] [INFO] Running command: blastn -query GCA_902754765.1_P1994_120_bin172_mag_fasta_genomic.fna/markers.fasta -db /var/lib/cwl/stgf04c3f13-d5b0-4f1d-92cc-8fdfa8a74775/dqc_reference/reference_markers_gtdb.fasta -out GCA_902754765.1_P1994_120_bin172_mag_fasta_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 18:27:42,997] [INFO] Task succeeded: Blastn
[2023-06-04 18:27:43,003] [INFO] Selected 28 target genomes.
[2023-06-04 18:27:43,004] [INFO] Target genome list was writen to GCA_902754765.1_P1994_120_bin172_mag_fasta_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 18:27:43,666] [INFO] Task started: fastANI
[2023-06-04 18:27:43,667] [INFO] Running command: fastANI --query /var/lib/cwl/stg42143281-b90a-4b02-b1a0-c1514147c744/GCA_902754765.1_P1994_120_bin172_mag_fasta_genomic.fna.gz --refList GCA_902754765.1_P1994_120_bin172_mag_fasta_genomic.fna/target_genomes_gtdb.txt --output GCA_902754765.1_P1994_120_bin172_mag_fasta_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 18:28:11,067] [INFO] Task succeeded: fastANI
[2023-06-04 18:28:11,091] [INFO] Found 28 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-04 18:28:11,092] [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_013390125.1	s__Mycobacterium hippocampi_A	82.0302	831	1266	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005222675.1	s__Mycobacterium sp005222675	81.9773	835	1266	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902705885.1	s__Mycobacterium vanbaalenii_A	81.7612	820	1266	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010723735.1	s__Mycobacterium hippocampi_B	81.7141	852	1266	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000266905.1	s__Mycobacterium chubuense_A	80.4014	720	1266	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	80.1828	779	1266	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.53	98.42	0.88	0.88	3	-
GCF_001545925.1	s__Mycobacterium sp001545925	80.1254	638	1266	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552715.1	s__Mycobacterium vaccae	80.0945	671	1266	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.97	1.00	1.00	3	-
GCA_000762985.1	s__Mycobacterium rufum_A	80.0388	719	1266	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001044255.1	s__Mycobacterium chubuense	79.9951	701	1266	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.8643	99.98	99.97	0.99	0.98	3	-
GCF_010726645.1	s__Mycobacterium duvalii	79.5559	664	1266	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001722335.1	s__Mycobacterium flavescens_A	79.4499	613	1266	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001672895.1	s__Mycobacterium sp001672895	79.0889	522	1266	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001499995.1	s__Mycobacterium sp001499995	79.034	573	1266	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620625.1	s__Mycobacterium sp000620625	78.9083	554	1266	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	78.8149	514	1266	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_010731815.2	s__Mycobacterium arabiense	78.7471	553	1266	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000328565.1	s__Mycobacterium sp000328565	78.6228	552	1266	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010727475.1	s__Mycobacterium mageritense	78.5741	538	1266	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.88	98.33	0.91	0.85	5	-
GCA_900078375.1	s__Mycobacterium sp900078375	78.5695	494	1266	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002887815.1	s__Mycobacterium sp002887815	78.5567	484	1266	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	78.5561	484	1266	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.54	98.54	0.94	0.94	2	-
GCA_017853185.1	s__Mycobacterium sp017853185	78.4876	375	1266	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001673535.1	s__Mycobacterium sp001673535	78.3831	444	1266	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	78.1066	376	1266	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903877095.1	s__Mycobacterium sp903877095	78.0208	410	1266	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.96	99.94	0.97	0.96	4	-
GCA_903884065.1	s__Mycobacterium sp903884065	78.0057	413	1266	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.70	99.70	0.92	0.92	2	-
GCA_005787665.1	s__Mycobacterium sp005787665	77.2011	254	1266	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 18:28:11,094] [INFO] GTDB search result was written to GCA_902754765.1_P1994_120_bin172_mag_fasta_genomic.fna/result_gtdb.tsv
[2023-06-04 18:28:11,094] [INFO] ===== GTDB Search completed =====
[2023-06-04 18:28:11,100] [INFO] DFAST_QC result json was written to GCA_902754765.1_P1994_120_bin172_mag_fasta_genomic.fna/dqc_result.json
[2023-06-04 18:28:11,101] [INFO] DFAST_QC completed!
[2023-06-04 18:28:11,101] [INFO] Total running time: 0h1m54s