[2024-01-24 13:40:35,016] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:35,020] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:35,020] [INFO] DQC Reference Directory: /var/lib/cwl/stg8f817b89-b2b5-435d-8395-f35505ef9c45/dqc_reference
[2024-01-24 13:40:36,434] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:36,435] [INFO] Task started: Prodigal
[2024-01-24 13:40:36,436] [INFO] Running command: gunzip -c /var/lib/cwl/stgb5e55b1e-8eb8-413b-aed7-a622c4bc0e54/GCF_025821665.1_ASM2582166v1_genomic.fna.gz | prodigal -d GCF_025821665.1_ASM2582166v1_genomic.fna/cds.fna -a GCF_025821665.1_ASM2582166v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:54,462] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:54,463] [INFO] Task started: HMMsearch
[2024-01-24 13:40:54,463] [INFO] Running command: hmmsearch --tblout GCF_025821665.1_ASM2582166v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8f817b89-b2b5-435d-8395-f35505ef9c45/dqc_reference/reference_markers.hmm GCF_025821665.1_ASM2582166v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:54,826] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:54,827] [INFO] Found 6/6 markers.
[2024-01-24 13:40:54,882] [INFO] Query marker FASTA was written to GCF_025821665.1_ASM2582166v1_genomic.fna/markers.fasta
[2024-01-24 13:40:54,882] [INFO] Task started: Blastn
[2024-01-24 13:40:54,882] [INFO] Running command: blastn -query GCF_025821665.1_ASM2582166v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f817b89-b2b5-435d-8395-f35505ef9c45/dqc_reference/reference_markers.fasta -out GCF_025821665.1_ASM2582166v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:56,336] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:56,345] [INFO] Selected 20 target genomes.
[2024-01-24 13:40:56,345] [INFO] Target genome list was writen to GCF_025821665.1_ASM2582166v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:56,364] [INFO] Task started: fastANI
[2024-01-24 13:40:56,365] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5e55b1e-8eb8-413b-aed7-a622c4bc0e54/GCF_025821665.1_ASM2582166v1_genomic.fna.gz --refList GCF_025821665.1_ASM2582166v1_genomic.fna/target_genomes.txt --output GCF_025821665.1_ASM2582166v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:22,973] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:22,974] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8f817b89-b2b5-435d-8395-f35505ef9c45/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:22,974] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8f817b89-b2b5-435d-8395-f35505ef9c45/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:22,992] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:41:22,992] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:41:22,992] [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 litorale	strain=JCM 17423	GCA_010731695.1	758802	758802	type	True	82.1729	1161	1928	95	below_threshold
Mycolicibacterium litorale	strain=CGMCC 4.5724	GCA_004366555.1	758802	758802	type	True	82.1423	1159	1928	95	below_threshold
Mycolicibacterium monacense	strain=DSM 44395	GCA_002086655.1	85693	85693	type	True	82.0314	1121	1928	95	below_threshold
Mycolicibacterium monacense	strain=JCM 15658	GCA_010731575.1	85693	85693	type	True	81.9764	1147	1928	95	below_threshold
Mycolicibacterium monacense	strain=DSM 44395	GCA_009931355.1	85693	85693	type	True	81.9637	1153	1928	95	below_threshold
Mycolicibacterium phlei	strain=DSM 43239 = CCUG 21000	GCA_001582015.1	1771	1771	type	True	81.8054	1067	1928	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_001583415.1	1771	1771	type	True	81.7791	1070	1928	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_009192875.1	1771	1771	type	True	81.7745	1076	1928	95	below_threshold
Mycolicibacterium rutilum	strain=DSM 45405	GCA_900108565.1	370526	370526	type	True	81.7507	1131	1928	95	below_threshold
Mycolicibacterium baixiangningiae	strain=LJ126	GCA_014893035.1	2761578	2761578	type	True	81.5596	1133	1928	95	below_threshold
Mycolicibacterium chubuense	strain=DSM 44219	GCA_001044255.1	1800	1800	type	True	81.3349	1071	1928	95	below_threshold
Mycolicibacterium chubuense	strain=NCTC10819	GCA_900453455.1	1800	1800	type	True	81.2485	1089	1928	95	below_threshold
Mycolicibacterium chubuense	strain=DSM 44219	GCA_002086595.1	1800	1800	type	True	81.2421	1082	1928	95	below_threshold
Mycobacterium doricum	strain=JCM 12405	GCA_010728155.1	126673	126673	type	True	81.1822	796	1928	95	below_threshold
Mycolicibacterium arabiense	strain=JCM 18538	GCA_010731815.2	1286181	1286181	type	True	80.9269	1109	1928	95	below_threshold
Mycolicibacterium lacusdiani	strain=JXJ CY 35	GCA_021916785.1	2895283	2895283	type	True	80.7908	1114	1928	95	below_threshold
Mycolicibacterium boenickei	strain=JCM 15653	GCA_010731295.1	146017	146017	type	True	80.4985	1008	1928	95	below_threshold
Mycolicibacterium anyangense	strain=JCM 30275	GCA_010731855.1	1431246	1431246	type	True	80.1259	838	1928	95	below_threshold
Mycolicibacterium fluoranthenivorans	strain=DSM 44556	GCA_011758805.1	258505	258505	type	True	80.0561	951	1928	95	below_threshold
Mycolicibacterium mengxianglii	strain=Z-34	GCA_015710575.2	2736649	2736649	type	True	79.6978	870	1928	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:22,994] [INFO] DFAST Taxonomy check result was written to GCF_025821665.1_ASM2582166v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:22,994] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:22,995] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:22,995] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8f817b89-b2b5-435d-8395-f35505ef9c45/dqc_reference/checkm_data
[2024-01-24 13:41:22,996] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:23,058] [INFO] Task started: CheckM
[2024-01-24 13:41:23,059] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025821665.1_ASM2582166v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025821665.1_ASM2582166v1_genomic.fna/checkm_input GCF_025821665.1_ASM2582166v1_genomic.fna/checkm_result
[2024-01-24 13:42:25,707] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:25,709] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:25,732] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:25,733] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:25,733] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025821665.1_ASM2582166v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:25,733] [INFO] Task started: Blastn
[2024-01-24 13:42:25,734] [INFO] Running command: blastn -query GCF_025821665.1_ASM2582166v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f817b89-b2b5-435d-8395-f35505ef9c45/dqc_reference/reference_markers_gtdb.fasta -out GCF_025821665.1_ASM2582166v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:27,932] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:27,937] [INFO] Selected 23 target genomes.
[2024-01-24 13:42:27,937] [INFO] Target genome list was writen to GCF_025821665.1_ASM2582166v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:27,966] [INFO] Task started: fastANI
[2024-01-24 13:42:27,966] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5e55b1e-8eb8-413b-aed7-a622c4bc0e54/GCF_025821665.1_ASM2582166v1_genomic.fna.gz --refList GCF_025821665.1_ASM2582166v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025821665.1_ASM2582166v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:56,013] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:56,033] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:42:56,033] [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_004570325.1	s__Mycobacterium sp004570325	82.4757	1151	1928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731695.1	s__Mycobacterium litorale	82.2017	1156	1928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010731575.1	s__Mycobacterium monacense	81.9811	1146	1928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.29	98.82	0.95	0.89	9	-
GCF_014218295.1	s__Mycobacterium litorale_B	81.9762	1123	1928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001499965.1	s__Mycobacterium sp001499965	81.9757	1151	1928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001500125.1	s__Mycobacterium sp001500125	81.9662	1128	1928	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	81.9298	1128	1928	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	81.7719	1072	1928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.86	99.38	0.98	0.91	10	-
GCF_900108565.1	s__Mycobacterium rutilum	81.7715	1126	1928	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	81.6528	1120	1928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017352375.1	s__Mycobacterium sp017352375	81.6333	1130	1928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016313185.1	s__Mycobacterium sp016313185	81.6092	1137	1928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.68	97.36	0.93	0.85	3	-
GCF_001665575.1	s__Mycobacterium sp001665575	81.5425	978	1928	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	81.3286	1072	1928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.8643	99.98	99.97	0.99	0.98	3	-
GCF_010729305.1	s__Mycobacterium psychrotolerans	81.194	1062	1928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.53	96.53	0.90	0.90	2	-
GCF_010728155.1	s__Mycobacterium doricum	81.1769	796	1928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001722355.1	s__Mycobacterium holsaticum	80.9838	918	1928	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	80.9286	1108	1928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731735.1	s__Mycobacterium sediminis	80.8044	1075	1928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001665535.1	s__Mycobacterium sp001665535	80.735	1021	1928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.97	96.97	0.90	0.90	2	-
GCF_001500025.1	s__Mycobacterium sp001500025	80.7196	1002	1928	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	80.6722	1031	1928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001668575.1	s__Mycobacterium sp001668575	80.6051	1003	1928	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 13:42:56,035] [INFO] GTDB search result was written to GCF_025821665.1_ASM2582166v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:56,036] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:56,040] [INFO] DFAST_QC result json was written to GCF_025821665.1_ASM2582166v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:56,041] [INFO] DFAST_QC completed!
[2024-01-24 13:42:56,041] [INFO] Total running time: 0h2m21s