[2024-01-24 12:40:50,466] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:50,470] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:50,471] [INFO] DQC Reference Directory: /var/lib/cwl/stge5d44bab-3c9b-4134-9da6-88c4a8c67566/dqc_reference
[2024-01-24 12:40:51,673] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:51,674] [INFO] Task started: Prodigal
[2024-01-24 12:40:51,674] [INFO] Running command: gunzip -c /var/lib/cwl/stgf95d419f-637f-4a95-91d5-9eec742e4b19/GCF_000333035.1_ASM33303v1_genomic.fna.gz | prodigal -d GCF_000333035.1_ASM33303v1_genomic.fna/cds.fna -a GCF_000333035.1_ASM33303v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:41:05,928] [INFO] Task succeeded: Prodigal
[2024-01-24 12:41:05,929] [INFO] Task started: HMMsearch
[2024-01-24 12:41:05,929] [INFO] Running command: hmmsearch --tblout GCF_000333035.1_ASM33303v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge5d44bab-3c9b-4134-9da6-88c4a8c67566/dqc_reference/reference_markers.hmm GCF_000333035.1_ASM33303v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:41:06,191] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:41:06,193] [INFO] Found 6/6 markers.
[2024-01-24 12:41:06,239] [INFO] Query marker FASTA was written to GCF_000333035.1_ASM33303v1_genomic.fna/markers.fasta
[2024-01-24 12:41:06,239] [INFO] Task started: Blastn
[2024-01-24 12:41:06,240] [INFO] Running command: blastn -query GCF_000333035.1_ASM33303v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge5d44bab-3c9b-4134-9da6-88c4a8c67566/dqc_reference/reference_markers.fasta -out GCF_000333035.1_ASM33303v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:07,361] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:07,365] [INFO] Selected 9 target genomes.
[2024-01-24 12:41:07,365] [INFO] Target genome list was writen to GCF_000333035.1_ASM33303v1_genomic.fna/target_genomes.txt
[2024-01-24 12:41:07,370] [INFO] Task started: fastANI
[2024-01-24 12:41:07,370] [INFO] Running command: fastANI --query /var/lib/cwl/stgf95d419f-637f-4a95-91d5-9eec742e4b19/GCF_000333035.1_ASM33303v1_genomic.fna.gz --refList GCF_000333035.1_ASM33303v1_genomic.fna/target_genomes.txt --output GCF_000333035.1_ASM33303v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:41:16,173] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:16,174] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge5d44bab-3c9b-4134-9da6-88c4a8c67566/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:41:16,175] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge5d44bab-3c9b-4134-9da6-88c4a8c67566/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:41:16,186] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:41:16,186] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:41:16,187] [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
Gordonia sihwensis	strain=NBRC 108236	GCA_000333035.1	173559	173559	type	True	100.0	1343	1349	95	conclusive
Gordonia neofelifaecis	strain=NRRL B-59395	GCA_000192435.2	945692	945692	type	True	83.6223	993	1349	95	below_threshold
Gordonia phthalatica	strain=QH-11	GCA_001305675.1	1136941	1136941	type	True	82.5723	901	1349	95	below_threshold
Gordonia hydrophobica	strain=NBRC 16057	GCA_001592365.1	40516	40516	type	True	81.7124	848	1349	95	below_threshold
Gordonia shandongensis	strain=DSM 45094	GCA_000423025.1	376351	376351	type	True	80.8997	712	1349	95	below_threshold
Gordonia spumicola	strain=NBRC 107696	GCA_009932475.1	589161	589161	type	True	80.7228	741	1349	95	below_threshold
Gordonia humi	strain=DSM 45298	GCA_014197435.1	686429	686429	type	True	80.2878	704	1349	95	below_threshold
Gordonia amarae	strain=NBRC 15530	GCA_000241345.2	36821	36821	type	True	78.6872	529	1349	95	below_threshold
Gordonia pseudamarae	strain=CON9	GCA_025273675.1	2831662	2831662	type	True	78.4907	469	1349	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:41:16,189] [INFO] DFAST Taxonomy check result was written to GCF_000333035.1_ASM33303v1_genomic.fna/tc_result.tsv
[2024-01-24 12:41:16,190] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:41:16,190] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:41:16,190] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge5d44bab-3c9b-4134-9da6-88c4a8c67566/dqc_reference/checkm_data
[2024-01-24 12:41:16,191] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:41:16,230] [INFO] Task started: CheckM
[2024-01-24 12:41:16,231] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000333035.1_ASM33303v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000333035.1_ASM33303v1_genomic.fna/checkm_input GCF_000333035.1_ASM33303v1_genomic.fna/checkm_result
[2024-01-24 12:42:01,834] [INFO] Task succeeded: CheckM
[2024-01-24 12:42:01,835] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:42:01,860] [INFO] ===== Completeness check finished =====
[2024-01-24 12:42:01,861] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:42:01,861] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000333035.1_ASM33303v1_genomic.fna/markers.fasta)
[2024-01-24 12:42:01,861] [INFO] Task started: Blastn
[2024-01-24 12:42:01,862] [INFO] Running command: blastn -query GCF_000333035.1_ASM33303v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge5d44bab-3c9b-4134-9da6-88c4a8c67566/dqc_reference/reference_markers_gtdb.fasta -out GCF_000333035.1_ASM33303v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:42:03,542] [INFO] Task succeeded: Blastn
[2024-01-24 12:42:03,546] [INFO] Selected 10 target genomes.
[2024-01-24 12:42:03,547] [INFO] Target genome list was writen to GCF_000333035.1_ASM33303v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:42:03,567] [INFO] Task started: fastANI
[2024-01-24 12:42:03,567] [INFO] Running command: fastANI --query /var/lib/cwl/stgf95d419f-637f-4a95-91d5-9eec742e4b19/GCF_000333035.1_ASM33303v1_genomic.fna.gz --refList GCF_000333035.1_ASM33303v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000333035.1_ASM33303v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:42:13,361] [INFO] Task succeeded: fastANI
[2024-01-24 12:42:13,375] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:42:13,375] [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_000333035.1	s__Gordonia sihwensis	100.0	1343	1349	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	99.38	98.97	0.93	0.88	4	conclusive
GCF_000192435.1	s__Gordonia neofelifaecis	83.6061	995	1349	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001305675.1	s__Gordonia phthalatica	82.615	896	1349	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001592365.1	s__Gordonia hydrophobica	81.7289	846	1349	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	100.00	100.00	1.00	1.00	2	-
GCA_012515855.1	s__Gordonia sp012515855	81.6079	745	1349	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423025.1	s__Gordonia shandongensis	80.923	709	1349	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009932475.1	s__Gordonia spumicola	80.6895	745	1349	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197435.1	s__Gordonia humi	80.2667	707	1349	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002700145.1	s__Gordonia sp002700145	78.7684	474	1349	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000241345.1	s__Gordonia amarae	78.6352	537	1349	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	99.98	99.98	0.99	0.99	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:42:13,377] [INFO] GTDB search result was written to GCF_000333035.1_ASM33303v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:42:13,377] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:42:13,380] [INFO] DFAST_QC result json was written to GCF_000333035.1_ASM33303v1_genomic.fna/dqc_result.json
[2024-01-24 12:42:13,381] [INFO] DFAST_QC completed!
[2024-01-24 12:42:13,381] [INFO] Total running time: 0h1m23s