[2024-01-24 11:05:28,186] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:28,188] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:28,189] [INFO] DQC Reference Directory: /var/lib/cwl/stg129b60af-aa8e-4ca7-b7c2-4d0fc70cfaa7/dqc_reference
[2024-01-24 11:05:29,645] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:29,651] [INFO] Task started: Prodigal
[2024-01-24 11:05:29,651] [INFO] Running command: gunzip -c /var/lib/cwl/stgfd6a5315-9b9d-4224-aad8-c1227bd4aae4/GCF_019645815.1_ASM1964581v1_genomic.fna.gz | prodigal -d GCF_019645815.1_ASM1964581v1_genomic.fna/cds.fna -a GCF_019645815.1_ASM1964581v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:48,622] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:48,622] [INFO] Task started: HMMsearch
[2024-01-24 11:05:48,623] [INFO] Running command: hmmsearch --tblout GCF_019645815.1_ASM1964581v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg129b60af-aa8e-4ca7-b7c2-4d0fc70cfaa7/dqc_reference/reference_markers.hmm GCF_019645815.1_ASM1964581v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:48,971] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:48,972] [INFO] Found 6/6 markers.
[2024-01-24 11:05:49,014] [INFO] Query marker FASTA was written to GCF_019645815.1_ASM1964581v1_genomic.fna/markers.fasta
[2024-01-24 11:05:49,014] [INFO] Task started: Blastn
[2024-01-24 11:05:49,014] [INFO] Running command: blastn -query GCF_019645815.1_ASM1964581v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg129b60af-aa8e-4ca7-b7c2-4d0fc70cfaa7/dqc_reference/reference_markers.fasta -out GCF_019645815.1_ASM1964581v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:50,161] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:50,164] [INFO] Selected 16 target genomes.
[2024-01-24 11:05:50,164] [INFO] Target genome list was writen to GCF_019645815.1_ASM1964581v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:50,169] [INFO] Task started: fastANI
[2024-01-24 11:05:50,170] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd6a5315-9b9d-4224-aad8-c1227bd4aae4/GCF_019645815.1_ASM1964581v1_genomic.fna.gz --refList GCF_019645815.1_ASM1964581v1_genomic.fna/target_genomes.txt --output GCF_019645815.1_ASM1964581v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:11,507] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:11,507] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg129b60af-aa8e-4ca7-b7c2-4d0fc70cfaa7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:11,508] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg129b60af-aa8e-4ca7-b7c2-4d0fc70cfaa7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:11,521] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:06:11,521] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:06:11,521] [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
Mycolicibacter nonchromogenicus	strain=DSM 44164	GCA_002101775.1	1782	1782	type	True	88.5257	1246	1687	95	below_threshold
Mycolicibacter longobardus	strain=DSM 45394	GCA_002102265.1	1108812	1108812	type	True	87.3604	1255	1687	95	below_threshold
Mycolicibacter engbaekii	strain=ATCC 27353	GCA_002101585.1	188915	188915	type	True	86.6831	1220	1687	95	below_threshold
Mycolicibacter hiberniae	strain=ATCC 49874	GCA_002101655.1	29314	29314	type	True	86.6708	1210	1687	95	below_threshold
Mycolicibacter hiberniae	strain=JCM 13571	GCA_010729485.1	29314	29314	type	True	86.5939	1225	1687	95	below_threshold
Mycolicibacter arupensis	strain=DSM 44942	GCA_002086515.1	342002	342002	type	True	86.2953	1166	1687	95	below_threshold
Mycolicibacter minnesotensis	strain=JCM 17932	GCA_010731755.1	1118379	1118379	type	True	86.2916	1202	1687	95	below_threshold
Mycolicibacter minnesotensis	strain=DSM 45633	GCA_002086405.1	1118379	1118379	type	True	86.2485	1193	1687	95	below_threshold
Mycolicibacter kumamotonensis	strain=DSM 45093	GCA_002086285.1	354243	354243	type	True	85.7941	1222	1687	95	below_threshold
Mycolicibacter terrae	strain=JCM 12143	GCA_010727125.1	1788	1788	type	True	85.561	1230	1687	95	below_threshold
Mycolicibacter kumamotonensis	strain=CST 7247	GCA_010093495.1	354243	354243	type	True	85.4835	1158	1687	95	below_threshold
Mycolicibacter senuensis	strain=JCM 16017	GCA_010723225.1	386913	386913	type	True	85.0869	1214	1687	95	below_threshold
Mycolicibacter senuensis	strain=DSM 44999	GCA_002101885.1	386913	386913	type	True	85.0424	1199	1687	95	below_threshold
Mycobacterium palustre	strain=DSM 44572	GCA_002101785.1	153971	153971	type	True	79.8321	769	1687	95	below_threshold
Mycobacterium noviomagense	strain=JCM 16367	GCA_010731635.1	459858	459858	type	True	79.1879	665	1687	95	below_threshold
Mycobacterium noviomagense	strain=DSM 45145	GCA_002086415.1	459858	459858	type	True	79.1649	657	1687	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:11,523] [INFO] DFAST Taxonomy check result was written to GCF_019645815.1_ASM1964581v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:11,524] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:11,524] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:11,524] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg129b60af-aa8e-4ca7-b7c2-4d0fc70cfaa7/dqc_reference/checkm_data
[2024-01-24 11:06:11,525] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:11,574] [INFO] Task started: CheckM
[2024-01-24 11:06:11,575] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019645815.1_ASM1964581v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019645815.1_ASM1964581v1_genomic.fna/checkm_input GCF_019645815.1_ASM1964581v1_genomic.fna/checkm_result
[2024-01-24 11:07:20,434] [INFO] Task succeeded: CheckM
[2024-01-24 11:07:20,436] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:07:20,457] [INFO] ===== Completeness check finished =====
[2024-01-24 11:07:20,457] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:07:20,458] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019645815.1_ASM1964581v1_genomic.fna/markers.fasta)
[2024-01-24 11:07:20,458] [INFO] Task started: Blastn
[2024-01-24 11:07:20,458] [INFO] Running command: blastn -query GCF_019645815.1_ASM1964581v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg129b60af-aa8e-4ca7-b7c2-4d0fc70cfaa7/dqc_reference/reference_markers_gtdb.fasta -out GCF_019645815.1_ASM1964581v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:07:22,071] [INFO] Task succeeded: Blastn
[2024-01-24 11:07:22,075] [INFO] Selected 13 target genomes.
[2024-01-24 11:07:22,076] [INFO] Target genome list was writen to GCF_019645815.1_ASM1964581v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:07:22,085] [INFO] Task started: fastANI
[2024-01-24 11:07:22,086] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd6a5315-9b9d-4224-aad8-c1227bd4aae4/GCF_019645815.1_ASM1964581v1_genomic.fna.gz --refList GCF_019645815.1_ASM1964581v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019645815.1_ASM1964581v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:07:42,133] [INFO] Task succeeded: fastANI
[2024-01-24 11:07:42,152] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:07:42,152] [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_001021505.1	s__Mycobacterium heraklionense_B	98.5788	1533	1687	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001673105.1	s__Mycobacterium heraklionense_A	90.3739	1381	1687	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.02	95.09	0.92	0.90	5	-
GCF_900078685.2	s__Mycobacterium icosiumassiliensis	90.2156	1272	1687	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000455125.1	s__Mycobacterium sp000455125	89.8101	1283	1687	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.70	98.55	0.90	0.88	3	-
GCF_002101775.1	s__Mycobacterium nonchromogenicum	88.4869	1251	1687	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.25	96.26	0.92	0.92	3	-
GCF_002102265.1	s__Mycobacterium longobardum	87.385	1251	1687	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667945.1	s__Mycobacterium sinense_B	85.6149	1189	1687	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.61	99.42	0.94	0.94	3	-
GCF_001667375.1	s__Mycobacterium sinense_A	85.4239	1189	1687	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.51	95.04	0.94	0.89	3	-
GCF_002086455.1	s__Mycobacterium algericum	85.2231	1184	1687	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.66	97.92	0.93	0.90	4	-
GCF_003284925.1	s__Mycobacterium algericum_A	85.1659	1043	1687	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002101885.1	s__Mycobacterium senuense	85.0378	1201	1687	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018455725.1	s__Mycobacterium sp018455725	82.5559	958	1687	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001665295.1	s__Mycobacterium sp001665295	79.6608	769	1687	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 11:07:42,154] [INFO] GTDB search result was written to GCF_019645815.1_ASM1964581v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:07:42,155] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:07:42,159] [INFO] DFAST_QC result json was written to GCF_019645815.1_ASM1964581v1_genomic.fna/dqc_result.json
[2024-01-24 11:07:42,159] [INFO] DFAST_QC completed!
[2024-01-24 11:07:42,159] [INFO] Total running time: 0h2m14s