[2024-01-24 14:03:01,730] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:03:01,731] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:03:01,732] [INFO] DQC Reference Directory: /var/lib/cwl/stg6254514b-dc4e-4acf-8965-3a74f4afea6a/dqc_reference
[2024-01-24 14:03:02,910] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:03:02,911] [INFO] Task started: Prodigal
[2024-01-24 14:03:02,911] [INFO] Running command: gunzip -c /var/lib/cwl/stg9b0cfd40-186d-42ae-8d39-7b8f4a9db9f4/GCF_013363975.1_ASM1336397v1_genomic.fna.gz | prodigal -d GCF_013363975.1_ASM1336397v1_genomic.fna/cds.fna -a GCF_013363975.1_ASM1336397v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:03:30,880] [INFO] Task succeeded: Prodigal
[2024-01-24 14:03:30,880] [INFO] Task started: HMMsearch
[2024-01-24 14:03:30,881] [INFO] Running command: hmmsearch --tblout GCF_013363975.1_ASM1336397v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6254514b-dc4e-4acf-8965-3a74f4afea6a/dqc_reference/reference_markers.hmm GCF_013363975.1_ASM1336397v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:03:31,337] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:03:31,338] [INFO] Found 6/6 markers.
[2024-01-24 14:03:31,431] [INFO] Query marker FASTA was written to GCF_013363975.1_ASM1336397v1_genomic.fna/markers.fasta
[2024-01-24 14:03:31,431] [INFO] Task started: Blastn
[2024-01-24 14:03:31,431] [INFO] Running command: blastn -query GCF_013363975.1_ASM1336397v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6254514b-dc4e-4acf-8965-3a74f4afea6a/dqc_reference/reference_markers.fasta -out GCF_013363975.1_ASM1336397v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:03:32,889] [INFO] Task succeeded: Blastn
[2024-01-24 14:03:32,892] [INFO] Selected 20 target genomes.
[2024-01-24 14:03:32,893] [INFO] Target genome list was writen to GCF_013363975.1_ASM1336397v1_genomic.fna/target_genomes.txt
[2024-01-24 14:03:32,902] [INFO] Task started: fastANI
[2024-01-24 14:03:32,902] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b0cfd40-186d-42ae-8d39-7b8f4a9db9f4/GCF_013363975.1_ASM1336397v1_genomic.fna.gz --refList GCF_013363975.1_ASM1336397v1_genomic.fna/target_genomes.txt --output GCF_013363975.1_ASM1336397v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:04:27,446] [INFO] Task succeeded: fastANI
[2024-01-24 14:04:27,446] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6254514b-dc4e-4acf-8965-3a74f4afea6a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:04:27,447] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6254514b-dc4e-4acf-8965-3a74f4afea6a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:04:27,461] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:04:27,461] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:04:27,462] [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
Nonomuraea montanisoli	strain=SMC 257	GCA_013363975.1	2741721	2741721	type	True	100.0	3224	3228	95	conclusive
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	94.4806	2766	3228	95	below_threshold
Nonomuraea muscovyensis	strain=DSM 45913	GCA_014207745.1	1124761	1124761	type	True	85.2889	2026	3228	95	below_threshold
Nonomuraea indica	strain=DRQ-2	GCA_002850745.1	1581193	1581193	type	True	85.1678	1896	3228	95	below_threshold
Nonomuraea lactucae	strain=NEAU-YG30	GCA_003313395.1	2249762	2249762	type	True	84.9809	1412	3228	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	84.1056	1212	3228	95	below_threshold
Nonomuraea cavernae	strain=SYSU K10005	GCA_020215905.1	2045107	2045107	type	True	84.0822	1683	3228	95	below_threshold
Nonomuraea cavernae	strain=CGMCC 4.7368	GCA_014646355.1	2045107	2045107	type	True	84.0474	1685	3228	95	below_threshold
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	83.6322	2044	3228	95	below_threshold
Nonomuraea jabiensis	strain=DSM 45507	GCA_014204795.1	882448	882448	type	True	83.4754	2135	3228	95	below_threshold
Nonomuraea angiospora	strain=DSM 43173	GCA_014873145.1	46172	46172	type	True	83.4633	2135	3228	95	below_threshold
Nonomuraea guangzhouensis	strain=CGMCC 4.7101	GCA_019396345.1	1291555	1291555	type	True	83.3951	2126	3228	95	below_threshold
Nonomuraea coxensis	strain=DSM 45129	GCA_019397265.1	404386	404386	type	True	83.3648	1817	3228	95	below_threshold
Nonomuraea phyllanthi	strain=PA1-10	GCA_006334985.2	2219224	2219224	type	True	83.1718	1945	3228	95	below_threshold
Nonomuraea harbinensis	strain=CGMCC 4.7106	GCA_019396385.1	1286938	1286938	type	True	83.0634	1763	3228	95	below_threshold
Nonomuraea basaltis	strain=160415	GCA_005893125.1	2495887	2495887	type	True	82.9975	1917	3228	95	below_threshold
Nonomuraea turkmeniaca	strain=DSM 43926	GCA_005889735.1	103838	103838	type	True	82.8775	1753	3228	95	below_threshold
Nonomuraea diastatica	strain=KC712	GCA_004349015.1	1848329	1848329	type	True	82.722	1715	3228	95	below_threshold
Nonomuraea dietziae	strain=DSM 44320	GCA_014195505.1	65515	65515	type	True	81.9491	1807	3228	95	below_threshold
Nonomuraea typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	81.8333	1810	3228	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:04:27,463] [INFO] DFAST Taxonomy check result was written to GCF_013363975.1_ASM1336397v1_genomic.fna/tc_result.tsv
[2024-01-24 14:04:27,464] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:04:27,464] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:04:27,464] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6254514b-dc4e-4acf-8965-3a74f4afea6a/dqc_reference/checkm_data
[2024-01-24 14:04:27,465] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:04:27,554] [INFO] Task started: CheckM
[2024-01-24 14:04:27,554] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013363975.1_ASM1336397v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013363975.1_ASM1336397v1_genomic.fna/checkm_input GCF_013363975.1_ASM1336397v1_genomic.fna/checkm_result
[2024-01-24 14:05:59,045] [INFO] Task succeeded: CheckM
[2024-01-24 14:05:59,047] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.07%
Contamintation: 5.67%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2024-01-24 14:05:59,072] [INFO] ===== Completeness check finished =====
[2024-01-24 14:05:59,073] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:05:59,073] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013363975.1_ASM1336397v1_genomic.fna/markers.fasta)
[2024-01-24 14:05:59,074] [INFO] Task started: Blastn
[2024-01-24 14:05:59,074] [INFO] Running command: blastn -query GCF_013363975.1_ASM1336397v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6254514b-dc4e-4acf-8965-3a74f4afea6a/dqc_reference/reference_markers_gtdb.fasta -out GCF_013363975.1_ASM1336397v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:01,415] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:01,419] [INFO] Selected 14 target genomes.
[2024-01-24 14:06:01,419] [INFO] Target genome list was writen to GCF_013363975.1_ASM1336397v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:01,494] [INFO] Task started: fastANI
[2024-01-24 14:06:01,494] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b0cfd40-186d-42ae-8d39-7b8f4a9db9f4/GCF_013363975.1_ASM1336397v1_genomic.fna.gz --refList GCF_013363975.1_ASM1336397v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013363975.1_ASM1336397v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:43,608] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:43,620] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:43,620] [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_013363975.1	s__Nonomuraea montanisoli	100.0	3224	3228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013363995.1	s__Nonomuraea rhodomycinica	94.5691	2696	3228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207745.1	s__Nonomuraea muscovyensis	85.261	2031	3228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002850745.1	s__Nonomuraea indica	85.1554	1900	3228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646355.1	s__Nonomuraea cavernae	84.0502	1685	3228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873145.1	s__Nonomuraea angiospora	83.4513	2139	3228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204795.1	s__Nonomuraea jabiensis	83.4505	2142	3228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379885.1	s__Nonomuraea coxensis	83.3298	1805	3228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006334985.2	s__Nonomuraea phyllanthi	83.1711	1945	3228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	99.34	99.34	0.97	0.97	2	-
GCF_008017515.1	s__Nonomuraea sp008017515	83.0789	1777	3228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005893125.1	s__Nonomuraea sp005893125	83.019	1912	3228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348685.1	s__Nonomuraea deserti	83.0047	1741	3228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	95.03	95.03	0.77	0.77	2	-
GCF_005889735.1	s__Nonomuraea turkmeniaca	82.8728	1754	3228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014195505.1	s__Nonomuraea dietziae	81.9328	1813	3228	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:06:43,625] [INFO] GTDB search result was written to GCF_013363975.1_ASM1336397v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:43,626] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:43,630] [INFO] DFAST_QC result json was written to GCF_013363975.1_ASM1336397v1_genomic.fna/dqc_result.json
[2024-01-24 14:06:43,631] [INFO] DFAST_QC completed!
[2024-01-24 14:06:43,631] [INFO] Total running time: 0h3m42s