[2024-01-24 11:43:42,422] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:42,430] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:42,430] [INFO] DQC Reference Directory: /var/lib/cwl/stg47d03461-9962-4d81-88a5-c7920099058b/dqc_reference
[2024-01-24 11:43:43,842] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:43,845] [INFO] Task started: Prodigal
[2024-01-24 11:43:43,845] [INFO] Running command: gunzip -c /var/lib/cwl/stg3db04ec9-ce17-4299-873e-69e156dac6cd/GCF_013409625.1_ASM1340962v1_genomic.fna.gz | prodigal -d GCF_013409625.1_ASM1340962v1_genomic.fna/cds.fna -a GCF_013409625.1_ASM1340962v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:59,662] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:59,663] [INFO] Task started: HMMsearch
[2024-01-24 11:43:59,663] [INFO] Running command: hmmsearch --tblout GCF_013409625.1_ASM1340962v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg47d03461-9962-4d81-88a5-c7920099058b/dqc_reference/reference_markers.hmm GCF_013409625.1_ASM1340962v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:00,112] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:00,113] [INFO] Found 6/6 markers.
[2024-01-24 11:44:00,162] [INFO] Query marker FASTA was written to GCF_013409625.1_ASM1340962v1_genomic.fna/markers.fasta
[2024-01-24 11:44:00,163] [INFO] Task started: Blastn
[2024-01-24 11:44:00,163] [INFO] Running command: blastn -query GCF_013409625.1_ASM1340962v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47d03461-9962-4d81-88a5-c7920099058b/dqc_reference/reference_markers.fasta -out GCF_013409625.1_ASM1340962v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:01,563] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:01,567] [INFO] Selected 13 target genomes.
[2024-01-24 11:44:01,567] [INFO] Target genome list was writen to GCF_013409625.1_ASM1340962v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:01,576] [INFO] Task started: fastANI
[2024-01-24 11:44:01,576] [INFO] Running command: fastANI --query /var/lib/cwl/stg3db04ec9-ce17-4299-873e-69e156dac6cd/GCF_013409625.1_ASM1340962v1_genomic.fna.gz --refList GCF_013409625.1_ASM1340962v1_genomic.fna/target_genomes.txt --output GCF_013409625.1_ASM1340962v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:21,879] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:21,879] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg47d03461-9962-4d81-88a5-c7920099058b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:21,880] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg47d03461-9962-4d81-88a5-c7920099058b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:21,892] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:21,892] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:21,892] [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
Nocardioides kongjuensis	strain=DSM 19082	GCA_013409625.1	349522	349522	type	True	100.0	1890	1891	95	conclusive
Nocardioides daeguensis	strain=2C1-5	GCA_019192965.1	908359	908359	type	True	89.3891	1211	1891	95	below_threshold
Nocardioides nitrophenolicus	strain=DSM 15529	GCA_016907515.1	60489	60489	type	True	89.119	1370	1891	95	below_threshold
Nocardioides albidus	strain=CCTCC AB 2015297	GCA_006335005.1	1517589	1517589	type	True	87.4354	1209	1891	95	below_threshold
Nocardioides humi	strain=DCY24	GCA_006494775.1	449461	449461	type	True	87.0271	1225	1891	95	below_threshold
Nocardioides carbamazepini	strain=CBZ_1	GCA_024614185.1	2854259	2854259	type	True	86.6576	1208	1891	95	below_threshold
Pimelobacter simplex	strain=NBRC 12069	GCA_006538965.1	2045	2045	type	True	85.7194	1251	1891	95	below_threshold
Pimelobacter simplex	strain=ATCC 6946	GCA_900114845.1	2045	2045	type	True	85.6771	1265	1891	95	below_threshold
Nocardioides aromaticivorans	strain=DSM 15131	GCA_013408525.1	200618	200618	type	True	85.4834	1226	1891	95	below_threshold
Nocardioides humilatus	strain=BN130099	GCA_008373755.1	2607660	2607660	type	True	81.5488	859	1891	95	below_threshold
Nocardioides sambongensis	strain=KUDC 5002	GCA_006494815.1	2589074	2589074	type	True	81.4017	853	1891	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	80.2655	784	1891	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	80.0834	670	1891	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:21,894] [INFO] DFAST Taxonomy check result was written to GCF_013409625.1_ASM1340962v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:21,894] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:21,895] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:21,895] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg47d03461-9962-4d81-88a5-c7920099058b/dqc_reference/checkm_data
[2024-01-24 11:44:21,896] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:21,950] [INFO] Task started: CheckM
[2024-01-24 11:44:21,950] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013409625.1_ASM1340962v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013409625.1_ASM1340962v1_genomic.fna/checkm_input GCF_013409625.1_ASM1340962v1_genomic.fna/checkm_result
[2024-01-24 11:45:58,170] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:58,172] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:58,194] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:58,195] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:58,195] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013409625.1_ASM1340962v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:58,195] [INFO] Task started: Blastn
[2024-01-24 11:45:58,195] [INFO] Running command: blastn -query GCF_013409625.1_ASM1340962v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47d03461-9962-4d81-88a5-c7920099058b/dqc_reference/reference_markers_gtdb.fasta -out GCF_013409625.1_ASM1340962v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:46:00,253] [INFO] Task succeeded: Blastn
[2024-01-24 11:46:00,257] [INFO] Selected 9 target genomes.
[2024-01-24 11:46:00,257] [INFO] Target genome list was writen to GCF_013409625.1_ASM1340962v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:46:00,266] [INFO] Task started: fastANI
[2024-01-24 11:46:00,266] [INFO] Running command: fastANI --query /var/lib/cwl/stg3db04ec9-ce17-4299-873e-69e156dac6cd/GCF_013409625.1_ASM1340962v1_genomic.fna.gz --refList GCF_013409625.1_ASM1340962v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013409625.1_ASM1340962v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:46:15,187] [INFO] Task succeeded: fastANI
[2024-01-24 11:46:15,206] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:46:15,206] [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_013409625.1	s__Nocardioides kongjuensis	100.0	1891	1891	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_006715725.1	s__Nocardioides sp006715725	91.0598	1464	1891	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016803235.1	s__Nocardioides simplex_A	90.5268	1422	1891	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019192965.1	s__Nocardioides daeguensis	89.3805	1212	1891	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907515.1	s__Nocardioides nitrophenolicus	89.1067	1371	1891	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006335005.1	s__Nocardioides albidus	87.4073	1211	1891	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006494775.1	s__Nocardioides humi	86.9866	1229	1891	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114845.1	s__Nocardioides simplex	85.7055	1262	1891	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.16	97.49	0.97	0.92	4	-
GCF_013408525.1	s__Nocardioides aromaticivorans	85.4995	1225	1891	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.43	98.36	0.91	0.91	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:46:15,209] [INFO] GTDB search result was written to GCF_013409625.1_ASM1340962v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:46:15,209] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:46:15,213] [INFO] DFAST_QC result json was written to GCF_013409625.1_ASM1340962v1_genomic.fna/dqc_result.json
[2024-01-24 11:46:15,213] [INFO] DFAST_QC completed!
[2024-01-24 11:46:15,214] [INFO] Total running time: 0h2m33s