[2024-01-24 13:41:20,354] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:20,356] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:20,356] [INFO] DQC Reference Directory: /var/lib/cwl/stgcde3c39b-69c1-4f7a-8fb6-163e4cae25f1/dqc_reference
[2024-01-24 13:41:21,760] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:21,761] [INFO] Task started: Prodigal
[2024-01-24 13:41:21,761] [INFO] Running command: gunzip -c /var/lib/cwl/stg9cba7b92-5c84-4a6d-8093-6fc7acbaac36/GCF_001552555.1_ASM155255v1_genomic.fna.gz | prodigal -d GCF_001552555.1_ASM155255v1_genomic.fna/cds.fna -a GCF_001552555.1_ASM155255v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:37,449] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:37,450] [INFO] Task started: HMMsearch
[2024-01-24 13:41:37,450] [INFO] Running command: hmmsearch --tblout GCF_001552555.1_ASM155255v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcde3c39b-69c1-4f7a-8fb6-163e4cae25f1/dqc_reference/reference_markers.hmm GCF_001552555.1_ASM155255v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:37,845] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:37,846] [INFO] Found 6/6 markers.
[2024-01-24 13:41:37,899] [INFO] Query marker FASTA was written to GCF_001552555.1_ASM155255v1_genomic.fna/markers.fasta
[2024-01-24 13:41:37,899] [INFO] Task started: Blastn
[2024-01-24 13:41:37,900] [INFO] Running command: blastn -query GCF_001552555.1_ASM155255v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcde3c39b-69c1-4f7a-8fb6-163e4cae25f1/dqc_reference/reference_markers.fasta -out GCF_001552555.1_ASM155255v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:39,297] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:39,300] [INFO] Selected 16 target genomes.
[2024-01-24 13:41:39,300] [INFO] Target genome list was writen to GCF_001552555.1_ASM155255v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:39,307] [INFO] Task started: fastANI
[2024-01-24 13:41:39,307] [INFO] Running command: fastANI --query /var/lib/cwl/stg9cba7b92-5c84-4a6d-8093-6fc7acbaac36/GCF_001552555.1_ASM155255v1_genomic.fna.gz --refList GCF_001552555.1_ASM155255v1_genomic.fna/target_genomes.txt --output GCF_001552555.1_ASM155255v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:42:02,328] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:02,329] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcde3c39b-69c1-4f7a-8fb6-163e4cae25f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:42:02,329] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcde3c39b-69c1-4f7a-8fb6-163e4cae25f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:42:02,344] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:42:02,344] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:42:02,344] [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
Nocardiopsis mwathae	strain=DSM 46659	GCA_014201195.1	1472723	1472723	type	True	81.5211	1038	1943	95	below_threshold
Nocardiopsis gilva	strain=YIM 90087	GCA_002263495.1	280236	280236	type	True	81.494	961	1943	95	below_threshold
Nocardiopsis gilva	strain=YIM 90087	GCA_000341165.1	280236	280236	type	True	81.4761	871	1943	95	below_threshold
Streptomonospora litoralis	strain=M2	GCA_004323735.1	2498135	2498135	type	True	81.2893	1036	1943	95	below_threshold
Streptomonospora alba	strain=YIM 90003	GCA_000826685.1	183763	183763	type	True	81.2161	1007	1943	95	below_threshold
Nocardiopsis potens	strain=DSM 45234	GCA_000341105.1	1246458	1246458	type	True	81.0744	1143	1943	95	below_threshold
Nocardiopsis composta	strain=DSM 44551	GCA_014200805.1	157465	157465	type	True	80.9982	1195	1943	95	below_threshold
Thermobifida cellulosilytica	strain=TB100	GCA_001517975.1	144786	144786	type	True	80.6174	797	1943	95	below_threshold
Thermobifida alba	strain=DSM 43795	GCA_023208015.1	53522	53522	type	True	80.2291	841	1943	95	below_threshold
Thermobifida halotolerans	strain=DSM 44931	GCA_003574835.2	483545	483545	type	True	80.1099	861	1943	95	below_threshold
Nocardiopsis sinuspersici	strain=UTMC 00102	GCA_001998325.1	501010	501010	type	True	80.107	928	1943	95	below_threshold
Thermobifida halotolerans	strain=YIM 90462	GCA_001660385.1	483545	483545	type	True	80.0486	850	1943	95	below_threshold
Nocardiopsis aegyptia	strain=DSM 44442	GCA_013410755.1	220378	220378	type	True	79.6547	1001	1943	95	below_threshold
Nocardiopsis metallicus	strain=DSM 44598	GCA_014201115.1	179819	179819	type	True	79.6401	877	1943	95	below_threshold
Nocardiopsis exhalans	strain=JCM11759T	GCA_024134545.1	163604	163604	type	True	79.6387	868	1943	95	below_threshold
Nocardiopsis listeri	strain=NBRC 13360	GCA_001570765.1	53440	53440	type	True	79.3492	738	1943	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:42:02,347] [INFO] DFAST Taxonomy check result was written to GCF_001552555.1_ASM155255v1_genomic.fna/tc_result.tsv
[2024-01-24 13:42:02,348] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:42:02,348] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:42:02,348] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcde3c39b-69c1-4f7a-8fb6-163e4cae25f1/dqc_reference/checkm_data
[2024-01-24 13:42:02,350] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:42:02,414] [INFO] Task started: CheckM
[2024-01-24 13:42:02,414] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001552555.1_ASM155255v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001552555.1_ASM155255v1_genomic.fna/checkm_input GCF_001552555.1_ASM155255v1_genomic.fna/checkm_result
[2024-01-24 13:43:10,817] [INFO] Task succeeded: CheckM
[2024-01-24 13:43:10,819] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:43:10,843] [INFO] ===== Completeness check finished =====
[2024-01-24 13:43:10,843] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:43:10,844] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001552555.1_ASM155255v1_genomic.fna/markers.fasta)
[2024-01-24 13:43:10,844] [INFO] Task started: Blastn
[2024-01-24 13:43:10,844] [INFO] Running command: blastn -query GCF_001552555.1_ASM155255v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcde3c39b-69c1-4f7a-8fb6-163e4cae25f1/dqc_reference/reference_markers_gtdb.fasta -out GCF_001552555.1_ASM155255v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:13,066] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:13,070] [INFO] Selected 15 target genomes.
[2024-01-24 13:43:13,071] [INFO] Target genome list was writen to GCF_001552555.1_ASM155255v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:43:13,111] [INFO] Task started: fastANI
[2024-01-24 13:43:13,111] [INFO] Running command: fastANI --query /var/lib/cwl/stg9cba7b92-5c84-4a6d-8093-6fc7acbaac36/GCF_001552555.1_ASM155255v1_genomic.fna.gz --refList GCF_001552555.1_ASM155255v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001552555.1_ASM155255v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:43:36,795] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:36,808] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:43:36,808] [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_001552555.1	s__Nocardiopsis_B trehalosi	100.0	1929	1943	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013410565.1	s__Streptomonospora nanhaiensis	82.459	1251	1943	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptomonospora	95.0	99.69	99.69	0.95	0.95	2	-
GCF_013408795.1	s__Spinactinospora alkalitolerans	81.7974	1108	1943	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spinactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009728995.1	s__Streptomonospora sp009728995	81.7149	1080	1943	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201195.1	s__Nocardiopsis_C mwathae	81.5737	1030	1943	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002263495.1	s__Nocardiopsis_C gilva	81.5068	959	1943	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_C	95.0	99.97	99.97	1.00	1.00	2	-
GCF_000341105.1	s__Nocardiopsis_A potens	81.1191	1136	1943	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200805.1	s__Nocardiopsis_A composta	81.0778	1180	1943	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003336425.1	s__Marinitenerispora sediminis	81.026	1007	1943	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Marinitenerispora	95.0	99.95	99.94	0.96	0.96	3	-
GCF_004363075.1	s__Actinorugispora endophytica	80.7829	952	1943	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Actinorugispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001517975.1	s__Thermobifida cellulosilytica	80.668	792	1943	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermobifida	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003014485.1	s__Murinocardiopsis flavida	80.5438	1109	1943	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Murinocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000981225.1	s__Allosalinactinospora lopnorensis	80.275	852	1943	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Allosalinactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001279585.1	s__Nocardiopsis sp001279585	79.9347	924	1943	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410755.1	s__Nocardiopsis aegyptia	79.7039	992	1943	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:43:36,810] [INFO] GTDB search result was written to GCF_001552555.1_ASM155255v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:43:36,810] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:43:36,814] [INFO] DFAST_QC result json was written to GCF_001552555.1_ASM155255v1_genomic.fna/dqc_result.json
[2024-01-24 13:43:36,814] [INFO] DFAST_QC completed!
[2024-01-24 13:43:36,814] [INFO] Total running time: 0h2m16s