[2024-01-24 10:57:38,949] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:38,951] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:38,951] [INFO] DQC Reference Directory: /var/lib/cwl/stg0077f68d-6d2d-4702-9c17-d392f4d3193d/dqc_reference
[2024-01-24 10:57:40,305] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:40,306] [INFO] Task started: Prodigal
[2024-01-24 10:57:40,306] [INFO] Running command: gunzip -c /var/lib/cwl/stge6b48fc4-1b26-41fb-a2b6-9c83b201a44b/GCF_014648355.1_ASM1464835v1_genomic.fna.gz | prodigal -d GCF_014648355.1_ASM1464835v1_genomic.fna/cds.fna -a GCF_014648355.1_ASM1464835v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:58:02,151] [INFO] Task succeeded: Prodigal
[2024-01-24 10:58:02,151] [INFO] Task started: HMMsearch
[2024-01-24 10:58:02,151] [INFO] Running command: hmmsearch --tblout GCF_014648355.1_ASM1464835v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0077f68d-6d2d-4702-9c17-d392f4d3193d/dqc_reference/reference_markers.hmm GCF_014648355.1_ASM1464835v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:58:02,510] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:58:02,512] [INFO] Found 6/6 markers.
[2024-01-24 10:58:02,572] [INFO] Query marker FASTA was written to GCF_014648355.1_ASM1464835v1_genomic.fna/markers.fasta
[2024-01-24 10:58:02,573] [INFO] Task started: Blastn
[2024-01-24 10:58:02,573] [INFO] Running command: blastn -query GCF_014648355.1_ASM1464835v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0077f68d-6d2d-4702-9c17-d392f4d3193d/dqc_reference/reference_markers.fasta -out GCF_014648355.1_ASM1464835v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:03,848] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:03,853] [INFO] Selected 18 target genomes.
[2024-01-24 10:58:03,853] [INFO] Target genome list was writen to GCF_014648355.1_ASM1464835v1_genomic.fna/target_genomes.txt
[2024-01-24 10:58:03,862] [INFO] Task started: fastANI
[2024-01-24 10:58:03,862] [INFO] Running command: fastANI --query /var/lib/cwl/stge6b48fc4-1b26-41fb-a2b6-9c83b201a44b/GCF_014648355.1_ASM1464835v1_genomic.fna.gz --refList GCF_014648355.1_ASM1464835v1_genomic.fna/target_genomes.txt --output GCF_014648355.1_ASM1464835v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:42,050] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:42,051] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0077f68d-6d2d-4702-9c17-d392f4d3193d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:42,051] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0077f68d-6d2d-4702-9c17-d392f4d3193d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:42,065] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:58:42,065] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:58:42,065] [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
Couchioplanes caeruleus	strain=DSM 43634	GCA_003751945.1	56438	56438	type	True	91.4957	2014	2515	95	below_threshold
Couchioplanes caeruleus subsp. caeruleus	strain=DSM 43634	GCA_001884705.1	56427	56438	type	True	91.4828	1821	2515	95	below_threshold
Actinoplanes nipponensis	strain=NBRC 14063	GCA_016862275.1	135950	135950	type	True	83.2896	1518	2515	95	below_threshold
Actinoplanes auranticolor	strain=NBRC 12245	GCA_018332655.1	47988	47988	type	True	83.013	1493	2515	95	below_threshold
Actinoplanes digitatis	strain=NBRC 12512	GCA_016862155.1	1868	1868	type	True	82.8945	1508	2515	95	below_threshold
Actinoplanes digitatis	strain=DSM 43149	GCA_014205335.1	1868	1868	type	True	82.8639	1548	2515	95	below_threshold
Actinoplanes friuliensis	strain=DSM 7358	GCA_000494755.1	196914	196914	type	True	82.4253	1438	2515	95	below_threshold
Actinoplanes consettensis	strain=NBRC 14913	GCA_018332715.1	113560	113560	type	True	81.9643	1380	2515	95	below_threshold
Actinoplanes humidus	strain=NBRC 14915	GCA_016862215.1	113566	113566	type	True	81.8868	1386	2515	95	below_threshold
Actinoplanes brasiliensis	strain=NBRC 13938	GCA_016862015.1	52695	52695	type	True	80.7121	1239	2515	95	below_threshold
Actinoplanes lichenicola	strain=LDG1-01	GCA_016785085.1	2802976	2802976	type	True	80.5425	1355	2515	95	below_threshold
Actinoplanes cyaneus	strain=NBRC 14990	GCA_016862095.1	52696	52696	type	True	80.2731	1276	2515	95	below_threshold
Actinoplanes flavus	strain=NEAU-H7	GCA_017592555.1	2820290	2820290	type	True	80.2167	1285	2515	95	below_threshold
Actinoplanes xinjiangensis	strain=DSM 45184	GCA_003148685.1	512350	512350	type	True	79.9901	1327	2515	95	below_threshold
Micromonospora phytophila	strain=DSM 105363	GCA_023656545.1	709888	709888	type	True	79.4287	832	2515	95	below_threshold
Dactylosporangium roseum	strain=NRRL B-16295	GCA_025264685.1	47989	47989	type	True	77.9234	892	2515	95	below_threshold
Dactylosporangium fulvum	strain=NRRL B-16292	GCA_025137375.1	53359	53359	type	True	77.8766	1011	2515	95	below_threshold
Dactylosporangium matsuzakiense	strain=NRRL B-16293	GCA_025264725.1	53360	53360	type	True	77.4661	1079	2515	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:42,067] [INFO] DFAST Taxonomy check result was written to GCF_014648355.1_ASM1464835v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:42,068] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:42,068] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:42,068] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0077f68d-6d2d-4702-9c17-d392f4d3193d/dqc_reference/checkm_data
[2024-01-24 10:58:42,069] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:42,136] [INFO] Task started: CheckM
[2024-01-24 10:58:42,137] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014648355.1_ASM1464835v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014648355.1_ASM1464835v1_genomic.fna/checkm_input GCF_014648355.1_ASM1464835v1_genomic.fna/checkm_result
[2024-01-24 10:59:59,222] [INFO] Task succeeded: CheckM
[2024-01-24 10:59:59,224] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:59:59,246] [INFO] ===== Completeness check finished =====
[2024-01-24 10:59:59,246] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:59:59,247] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014648355.1_ASM1464835v1_genomic.fna/markers.fasta)
[2024-01-24 10:59:59,247] [INFO] Task started: Blastn
[2024-01-24 10:59:59,247] [INFO] Running command: blastn -query GCF_014648355.1_ASM1464835v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0077f68d-6d2d-4702-9c17-d392f4d3193d/dqc_reference/reference_markers_gtdb.fasta -out GCF_014648355.1_ASM1464835v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:00:01,215] [INFO] Task succeeded: Blastn
[2024-01-24 11:00:01,218] [INFO] Selected 9 target genomes.
[2024-01-24 11:00:01,219] [INFO] Target genome list was writen to GCF_014648355.1_ASM1464835v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:00:01,225] [INFO] Task started: fastANI
[2024-01-24 11:00:01,225] [INFO] Running command: fastANI --query /var/lib/cwl/stge6b48fc4-1b26-41fb-a2b6-9c83b201a44b/GCF_014648355.1_ASM1464835v1_genomic.fna.gz --refList GCF_014648355.1_ASM1464835v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014648355.1_ASM1464835v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:00:22,533] [INFO] Task succeeded: fastANI
[2024-01-24 11:00:22,547] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:00:22,547] [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_014648355.1	s__Actinoplanes azureus	100.0	2515	2515	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003751945.1	s__Actinoplanes caeruleus	91.5398	2008	2515	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.99	99.99	0.98	0.98	2	-
GCF_003002065.1	s__Actinoplanes ferrugineus_A	85.2072	1557	2515	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.31	99.31	0.94	0.94	2	-
GCF_016464385.1	s__Actinoplanes sp016464385	84.3407	1545	2515	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862275.1	s__Actinoplanes nipponensis	83.2665	1521	2515	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205335.1	s__Actinoplanes digitatis	82.891	1542	2515	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000389965.1	s__Actinoplanes sp000389965	82.3652	1452	2515	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018332715.1	s__Actinoplanes consettensis	81.9894	1376	2515	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148685.1	s__Actinoplanes xinjiangensis	79.9285	1343	2515	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:00:22,549] [INFO] GTDB search result was written to GCF_014648355.1_ASM1464835v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:00:22,549] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:00:22,553] [INFO] DFAST_QC result json was written to GCF_014648355.1_ASM1464835v1_genomic.fna/dqc_result.json
[2024-01-24 11:00:22,553] [INFO] DFAST_QC completed!
[2024-01-24 11:00:22,553] [INFO] Total running time: 0h2m44s