[2024-01-24 14:02:51,497] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:02:51,501] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:02:51,501] [INFO] DQC Reference Directory: /var/lib/cwl/stgb3dca745-ef20-48b0-a341-7cb0e8508f47/dqc_reference
[2024-01-24 14:02:52,969] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:02:52,970] [INFO] Task started: Prodigal
[2024-01-24 14:02:52,971] [INFO] Running command: gunzip -c /var/lib/cwl/stgf6fecf41-9e47-4c8e-b9a1-f117e76879ae/GCF_008329645.1_ASM832964v1_genomic.fna.gz | prodigal -d GCF_008329645.1_ASM832964v1_genomic.fna/cds.fna -a GCF_008329645.1_ASM832964v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:03:10,980] [INFO] Task succeeded: Prodigal
[2024-01-24 14:03:10,980] [INFO] Task started: HMMsearch
[2024-01-24 14:03:10,980] [INFO] Running command: hmmsearch --tblout GCF_008329645.1_ASM832964v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb3dca745-ef20-48b0-a341-7cb0e8508f47/dqc_reference/reference_markers.hmm GCF_008329645.1_ASM832964v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:03:11,304] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:03:11,305] [INFO] Found 6/6 markers.
[2024-01-24 14:03:11,353] [INFO] Query marker FASTA was written to GCF_008329645.1_ASM832964v1_genomic.fna/markers.fasta
[2024-01-24 14:03:11,354] [INFO] Task started: Blastn
[2024-01-24 14:03:11,354] [INFO] Running command: blastn -query GCF_008329645.1_ASM832964v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3dca745-ef20-48b0-a341-7cb0e8508f47/dqc_reference/reference_markers.fasta -out GCF_008329645.1_ASM832964v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:03:12,722] [INFO] Task succeeded: Blastn
[2024-01-24 14:03:12,726] [INFO] Selected 23 target genomes.
[2024-01-24 14:03:12,727] [INFO] Target genome list was writen to GCF_008329645.1_ASM832964v1_genomic.fna/target_genomes.txt
[2024-01-24 14:03:12,738] [INFO] Task started: fastANI
[2024-01-24 14:03:12,738] [INFO] Running command: fastANI --query /var/lib/cwl/stgf6fecf41-9e47-4c8e-b9a1-f117e76879ae/GCF_008329645.1_ASM832964v1_genomic.fna.gz --refList GCF_008329645.1_ASM832964v1_genomic.fna/target_genomes.txt --output GCF_008329645.1_ASM832964v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:03:42,650] [INFO] Task succeeded: fastANI
[2024-01-24 14:03:42,651] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb3dca745-ef20-48b0-a341-7cb0e8508f47/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:03:42,652] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb3dca745-ef20-48b0-a341-7cb0e8508f47/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:03:42,672] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:03:42,672] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:03:42,672] [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 arabiense	strain=JCM 18538	GCA_010731815.2	1286181	1286181	type	True	82.8185	1360	1893	95	below_threshold
Mycolicibacterium lacusdiani	strain=JXJ CY 35	GCA_021916785.1	2895283	2895283	type	True	82.7949	1335	1893	95	below_threshold
Mycolicibacterium phlei	strain=DSM 43239 = CCUG 21000	GCA_001582015.1	1771	1771	type	True	81.5351	1044	1893	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_009192875.1	1771	1771	type	True	81.5323	1036	1893	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_001583415.1	1771	1771	type	True	81.4657	1062	1893	95	below_threshold
Mycolicibacterium rutilum	strain=DSM 45405	GCA_900108565.1	370526	370526	type	True	81.3419	1093	1893	95	below_threshold
Mycolicibacterium chubuense	strain=DSM 44219	GCA_001044255.1	1800	1800	type	True	81.2008	1084	1893	95	below_threshold
Mycolicibacterium litorale	strain=JCM 17423	GCA_010731695.1	758802	758802	type	True	81.1675	1099	1893	95	below_threshold
Mycolicibacterium chubuense	strain=DSM 44219	GCA_002086595.1	1800	1800	type	True	81.1599	1102	1893	95	below_threshold
Mycolicibacterium chlorophenolicum	strain=DSM 43826	GCA_001044235.1	37916	37916	type	True	81.1509	1143	1893	95	below_threshold
Mycolicibacterium litorale	strain=CGMCC 4.5724	GCA_004366555.1	758802	758802	type	True	81.089	1107	1893	95	below_threshold
Mycolicibacterium chubuense	strain=NCTC10819	GCA_900453455.1	1800	1800	type	True	81.0659	1130	1893	95	below_threshold
Mycolicibacterium chlorophenolicum	strain=NBRC 15527	GCA_001552315.1	37916	37916	type	True	81.0557	1148	1893	95	below_threshold
Mycolicibacterium psychrotolerans	strain=JCM 13323	GCA_010729305.1	216929	216929	type	True	81.0439	1045	1893	95	below_threshold
Mycolicibacterium cosmeticum	strain=DSM 44829	GCA_000613185.1	258533	258533	type	True	80.8118	1071	1893	95	below_threshold
Mycolicibacterium cosmeticum	strain=DSM 44829	GCA_005670675.1	258533	258533	type	True	80.7492	1062	1893	95	below_threshold
Mycolicibacterium phocaicum	strain=JCM 15301	GCA_010731115.1	319706	319706	type	True	80.4994	884	1893	95	below_threshold
Mycolicibacterium llatzerense	strain=MG13	GCA_025331195.1	280871	280871	type	True	80.2595	868	1893	95	below_threshold
Mycolicibacterium aurum	strain=NCTC10437	GCA_900637195.1	1791	1791	type	True	80.1548	1015	1893	95	below_threshold
Mycolicibacterium aurum	strain=NCTC 10437	GCA_001049355.1	1791	1791	type	True	80.1294	1011	1893	95	below_threshold
Mycolicibacterium mageritense	strain=CIP 104973	GCA_000612825.1	53462	53462	type	True	80.0809	1064	1893	95	below_threshold
Mycolicibacterium mageritense	strain=JCM 12375	GCA_010727475.1	53462	53462	type	True	80.0376	1063	1893	95	below_threshold
Mycolicibacterium brumae	strain=ATCC 51384	GCA_025215495.1	85968	85968	type	True	80.019	695	1893	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:03:42,674] [INFO] DFAST Taxonomy check result was written to GCF_008329645.1_ASM832964v1_genomic.fna/tc_result.tsv
[2024-01-24 14:03:42,674] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:03:42,674] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:03:42,675] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb3dca745-ef20-48b0-a341-7cb0e8508f47/dqc_reference/checkm_data
[2024-01-24 14:03:42,675] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:03:42,732] [INFO] Task started: CheckM
[2024-01-24 14:03:42,732] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008329645.1_ASM832964v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008329645.1_ASM832964v1_genomic.fna/checkm_input GCF_008329645.1_ASM832964v1_genomic.fna/checkm_result
[2024-01-24 14:04:59,575] [INFO] Task succeeded: CheckM
[2024-01-24 14:04:59,577] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:04:59,598] [INFO] ===== Completeness check finished =====
[2024-01-24 14:04:59,598] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:04:59,599] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008329645.1_ASM832964v1_genomic.fna/markers.fasta)
[2024-01-24 14:04:59,599] [INFO] Task started: Blastn
[2024-01-24 14:04:59,599] [INFO] Running command: blastn -query GCF_008329645.1_ASM832964v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3dca745-ef20-48b0-a341-7cb0e8508f47/dqc_reference/reference_markers_gtdb.fasta -out GCF_008329645.1_ASM832964v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:01,660] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:01,665] [INFO] Selected 23 target genomes.
[2024-01-24 14:05:01,665] [INFO] Target genome list was writen to GCF_008329645.1_ASM832964v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:05:01,779] [INFO] Task started: fastANI
[2024-01-24 14:05:01,780] [INFO] Running command: fastANI --query /var/lib/cwl/stgf6fecf41-9e47-4c8e-b9a1-f117e76879ae/GCF_008329645.1_ASM832964v1_genomic.fna.gz --refList GCF_008329645.1_ASM832964v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008329645.1_ASM832964v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:05:33,174] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:33,200] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:05:33,200] [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_008329645.1	s__Mycobacterium grossiae	100.0	1890	1893	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.93	99.93	0.94	0.94	2	conclusive
GCF_010731735.1	s__Mycobacterium sediminis	82.9277	1326	1893	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731815.2	s__Mycobacterium arabiense	82.8054	1360	1893	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004570325.1	s__Mycobacterium sp004570325	81.4392	1107	1893	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	81.4303	1067	1893	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.86	99.38	0.98	0.91	10	-
GCF_008329535.1	s__Mycobacterium sp008329535	81.3223	1150	1893	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000762985.1	s__Mycobacterium rufum_A	81.2872	1108	1893	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	81.1914	1087	1893	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.8643	99.98	99.97	0.99	0.98	3	-
GCF_001044235.1	s__Mycobacterium chlorophenolicum	81.1403	1145	1893	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.8643	98.88	97.93	0.94	0.90	4	-
GCF_014218295.1	s__Mycobacterium litorale_B	81.1228	1072	1893	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	81.0819	1033	1893	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010729305.1	s__Mycobacterium psychrotolerans	81.06	1043	1893	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.53	96.53	0.90	0.90	2	-
GCF_001545925.1	s__Mycobacterium sp001545925	81.0076	900	1893	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007096635.1	s__Mycobacterium sp007096635	80.8736	1006	1893	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001426545.1	s__Mycobacterium sp001426545	80.8473	1102	1893	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010725485.1	s__Mycobacterium sp002946335	80.8076	1019	1893	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.86	98.86	0.96	0.96	2	-
GCF_002086815.1	s__Mycobacterium parafortuitum	80.7584	1037	1893	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017352375.1	s__Mycobacterium sp017352375	80.5133	1071	1893	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	80.4619	1046	1893	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.88	98.06	0.95	0.91	32	-
GCF_005670685.2	s__Mycobacterium mucogenicum_B	80.4278	920	1893	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.72	96.94	0.94	0.86	7	-
GCF_010727475.1	s__Mycobacterium mageritense	80.0603	1063	1893	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.88	98.33	0.91	0.85	5	-
GCF_002723835.1	s__Mycobacterium sp002723835	80.0442	916	1893	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667505.1	s__Mycobacterium sp001667505	79.8842	995	1893	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:05:33,202] [INFO] GTDB search result was written to GCF_008329645.1_ASM832964v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:05:33,202] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:05:33,207] [INFO] DFAST_QC result json was written to GCF_008329645.1_ASM832964v1_genomic.fna/dqc_result.json
[2024-01-24 14:05:33,207] [INFO] DFAST_QC completed!
[2024-01-24 14:05:33,207] [INFO] Total running time: 0h2m42s