[2024-01-24 14:47:55,934] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:47:55,935] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:47:55,935] [INFO] DQC Reference Directory: /var/lib/cwl/stg8f323a3c-9508-42ad-82ac-e448ad53f3df/dqc_reference
[2024-01-24 14:47:58,525] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:47:58,526] [INFO] Task started: Prodigal
[2024-01-24 14:47:58,526] [INFO] Running command: gunzip -c /var/lib/cwl/stgd675215c-ff35-47e7-9eef-cd6da05953fc/GCF_013761175.1_ASM1376117v1_genomic.fna.gz | prodigal -d GCF_013761175.1_ASM1376117v1_genomic.fna/cds.fna -a GCF_013761175.1_ASM1376117v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:48:33,642] [INFO] Task succeeded: Prodigal
[2024-01-24 14:48:33,642] [INFO] Task started: HMMsearch
[2024-01-24 14:48:33,642] [INFO] Running command: hmmsearch --tblout GCF_013761175.1_ASM1376117v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8f323a3c-9508-42ad-82ac-e448ad53f3df/dqc_reference/reference_markers.hmm GCF_013761175.1_ASM1376117v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:48:34,091] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:48:34,093] [INFO] Found 6/6 markers.
[2024-01-24 14:48:34,177] [INFO] Query marker FASTA was written to GCF_013761175.1_ASM1376117v1_genomic.fna/markers.fasta
[2024-01-24 14:48:34,178] [INFO] Task started: Blastn
[2024-01-24 14:48:34,178] [INFO] Running command: blastn -query GCF_013761175.1_ASM1376117v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f323a3c-9508-42ad-82ac-e448ad53f3df/dqc_reference/reference_markers.fasta -out GCF_013761175.1_ASM1376117v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:35,635] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:35,639] [INFO] Selected 29 target genomes.
[2024-01-24 14:48:35,640] [INFO] Target genome list was writen to GCF_013761175.1_ASM1376117v1_genomic.fna/target_genomes.txt
[2024-01-24 14:48:35,665] [INFO] Task started: fastANI
[2024-01-24 14:48:35,665] [INFO] Running command: fastANI --query /var/lib/cwl/stgd675215c-ff35-47e7-9eef-cd6da05953fc/GCF_013761175.1_ASM1376117v1_genomic.fna.gz --refList GCF_013761175.1_ASM1376117v1_genomic.fna/target_genomes.txt --output GCF_013761175.1_ASM1376117v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:49:37,907] [INFO] Task succeeded: fastANI
[2024-01-24 14:49:37,908] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8f323a3c-9508-42ad-82ac-e448ad53f3df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:49:37,908] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8f323a3c-9508-42ad-82ac-e448ad53f3df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:49:37,936] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:49:37,936] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:49:37,937] [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 africana	strain=DSM 43748	GCA_014873535.1	46171	46171	type	True	81.4138	1732	3353	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	81.345	1106	3353	95	below_threshold
Nonomuraea dietziae	strain=DSM 44320	GCA_014195505.1	65515	65515	type	True	81.2961	1759	3353	95	below_threshold
Nonomuraea endophytica	strain=DSM 45385	GCA_014203235.1	714136	714136	type	True	81.2058	1863	3353	95	below_threshold
Nonomuraea antri	strain=NN258	GCA_013283785.1	2730852	2730852	type	True	81.1872	1768	3353	95	below_threshold
Nonomuraea cavernae	strain=SYSU K10005	GCA_020215905.1	2045107	2045107	type	True	81.161	1505	3353	95	below_threshold
Nonomuraea ceibae	strain=KCTC 39826	GCA_019396325.1	1935170	1935170	type	True	81.124	1693	3353	95	below_threshold
Nonomuraea cavernae	strain=CGMCC 4.7368	GCA_014646355.1	2045107	2045107	type	True	81.1192	1507	3353	95	below_threshold
Nonomuraea harbinensis	strain=CGMCC 4.7106	GCA_019396385.1	1286938	1286938	type	True	81.1133	1629	3353	95	below_threshold
Nonomuraea typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	81.1089	1818	3353	95	below_threshold
Nonomuraea indica	strain=DRQ-2	GCA_002850745.1	1581193	1581193	type	True	81.0626	1550	3353	95	below_threshold
Nonomuraea lactucae	strain=NEAU-YG30	GCA_003313395.1	2249762	2249762	type	True	81.0582	1246	3353	95	below_threshold
Nonomuraea coxensis	strain=DSM 45129	GCA_000379885.1	404386	404386	type	True	81.0299	1625	3353	95	below_threshold
Nonomuraea muscovyensis	strain=DSM 45913	GCA_014207745.1	1124761	1124761	type	True	81.0261	1637	3353	95	below_threshold
Nonomuraea coxensis	strain=DSM 45129	GCA_019397265.1	404386	404386	type	True	80.9794	1642	3353	95	below_threshold
Nonomuraea wenchangensis	strain=CGMCC 4.5598	GCA_900111685.1	568860	568860	type	True	80.9794	1680	3353	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	80.8335	1671	3353	95	below_threshold
Nonomuraea fuscirosea	strain=CGMCC 4.7104	GCA_003001935.1	1291556	1291556	type	True	80.7944	1741	3353	95	below_threshold
Nonomuraea spiralis	strain=JCM 3286	GCA_014648435.1	46182	46182	type	True	80.7518	1790	3353	95	below_threshold
Nonomuraea zeae	strain=DSM 100528	GCA_005889725.1	1642303	1642303	type	True	80.6792	1807	3353	95	below_threshold
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	80.6438	1683	3353	95	below_threshold
Nonomuraea basaltis	strain=160415	GCA_005893125.1	2495887	2495887	type	True	80.4711	1702	3353	95	below_threshold
Nonomuraea guangzhouensis	strain=CGMCC 4.7101	GCA_019396345.1	1291555	1291555	type	True	80.4061	1755	3353	95	below_threshold
Sphaerisporangium siamense	strain=DSM 45784	GCA_014205275.1	795645	795645	type	True	79.0912	1195	3353	95	below_threshold
Sphaerisporangium siamense	strain=NBRC 107570	GCA_016863415.1	795645	795645	type	True	78.9458	1209	3353	95	below_threshold
Streptomyces fradiae	strain=NRRL B-1195	GCA_002154445.1	1906	1906	suspected-type	True	77.0706	502	3353	95	below_threshold
Streptomyces fradiae	strain=ATCC 10745	GCA_008704425.1	1906	1906	suspected-type	True	76.7708	732	3353	95	below_threshold
Streptomyces fradiae	strain=DSM 40063	GCA_002119225.1	1906	1906	suspected-type	True	76.742	693	3353	95	below_threshold
Streptomyces fradiae	strain=ATCC 10745	GCA_009834665.1	1906	1906	suspected-type	True	76.7408	720	3353	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:49:37,939] [INFO] DFAST Taxonomy check result was written to GCF_013761175.1_ASM1376117v1_genomic.fna/tc_result.tsv
[2024-01-24 14:49:37,939] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:49:37,940] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:49:37,940] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8f323a3c-9508-42ad-82ac-e448ad53f3df/dqc_reference/checkm_data
[2024-01-24 14:49:37,941] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:49:38,051] [INFO] Task started: CheckM
[2024-01-24 14:49:38,051] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013761175.1_ASM1376117v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013761175.1_ASM1376117v1_genomic.fna/checkm_input GCF_013761175.1_ASM1376117v1_genomic.fna/checkm_result
[2024-01-24 14:51:33,343] [INFO] Task succeeded: CheckM
[2024-01-24 14:51:33,344] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:51:33,373] [INFO] ===== Completeness check finished =====
[2024-01-24 14:51:33,373] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:51:33,374] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013761175.1_ASM1376117v1_genomic.fna/markers.fasta)
[2024-01-24 14:51:33,375] [INFO] Task started: Blastn
[2024-01-24 14:51:33,375] [INFO] Running command: blastn -query GCF_013761175.1_ASM1376117v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f323a3c-9508-42ad-82ac-e448ad53f3df/dqc_reference/reference_markers_gtdb.fasta -out GCF_013761175.1_ASM1376117v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:51:35,570] [INFO] Task succeeded: Blastn
[2024-01-24 14:51:35,574] [INFO] Selected 22 target genomes.
[2024-01-24 14:51:35,575] [INFO] Target genome list was writen to GCF_013761175.1_ASM1376117v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:51:35,595] [INFO] Task started: fastANI
[2024-01-24 14:51:35,596] [INFO] Running command: fastANI --query /var/lib/cwl/stgd675215c-ff35-47e7-9eef-cd6da05953fc/GCF_013761175.1_ASM1376117v1_genomic.fna.gz --refList GCF_013761175.1_ASM1376117v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013761175.1_ASM1376117v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:52:34,307] [INFO] Task succeeded: fastANI
[2024-01-24 14:52:34,325] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:52:34,326] [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_013761175.1	s__Nonomuraea soli	100.0	3350	3353	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_002093975.1	s__Nonomuraea rubra_A	82.4931	1740	3353	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873535.1	s__Nonomuraea africana	81.4001	1737	3353	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	81.2966	1758	3353	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203235.1	s__Nonomuraea endophytica	81.2306	1861	3353	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001083785.1	s__Nonomuraea sp001083785	81.2009	1631	3353	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013283785.1	s__Nonomuraea sp013283785	81.1705	1772	3353	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	81.1338	1504	3353	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	81.056	1551	3353	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	81.0358	1634	3353	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111685.1	s__Nonomuraea wenchangensis	81.0302	1671	3353	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018531495.1	s__Nonomuraea sp018531495	81.0158	1785	3353	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008017515.1	s__Nonomuraea sp008017515	80.993	1671	3353	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	80.9854	1635	3353	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013363975.1	s__Nonomuraea montanisoli	80.8007	1656	3353	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003001935.1	s__Nonomuraea fuscirosea	80.7705	1750	3353	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648435.1	s__Nonomuraea spiralis	80.7682	1783	3353	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	98.03	98.03	0.91	0.91	2	-
GCF_005889725.1	s__Nonomuraea zeae	80.6538	1817	3353	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900323885.1	s__Nonomuraea parvosata	80.631	1917	3353	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	98.64	97.29	0.94	0.90	3	-
GCF_014202315.1	s__Thermocatellispora tengchongensis	79.601	1588	3353	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermocatellispora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003242605.1	s__Thermopolyspora sp003242605	78.5562	880	3353	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007595705.1	s__Streptomyces sp007595705	76.6057	776	3353	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:52:34,327] [INFO] GTDB search result was written to GCF_013761175.1_ASM1376117v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:52:34,328] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:52:34,333] [INFO] DFAST_QC result json was written to GCF_013761175.1_ASM1376117v1_genomic.fna/dqc_result.json
[2024-01-24 14:52:34,333] [INFO] DFAST_QC completed!
[2024-01-24 14:52:34,333] [INFO] Total running time: 0h4m38s