[2024-01-24 13:21:46,233] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:46,235] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:46,236] [INFO] DQC Reference Directory: /var/lib/cwl/stg3e7a8704-1dad-4afd-8d6c-565456a935a2/dqc_reference
[2024-01-24 13:21:47,657] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:21:47,658] [INFO] Task started: Prodigal
[2024-01-24 13:21:47,659] [INFO] Running command: gunzip -c /var/lib/cwl/stg7b59f691-8532-4b41-bd16-3118865feb63/GCF_015070375.1_ASM1507037v1_genomic.fna.gz | prodigal -d GCF_015070375.1_ASM1507037v1_genomic.fna/cds.fna -a GCF_015070375.1_ASM1507037v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:21:59,091] [INFO] Task succeeded: Prodigal
[2024-01-24 13:21:59,092] [INFO] Task started: HMMsearch
[2024-01-24 13:21:59,092] [INFO] Running command: hmmsearch --tblout GCF_015070375.1_ASM1507037v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3e7a8704-1dad-4afd-8d6c-565456a935a2/dqc_reference/reference_markers.hmm GCF_015070375.1_ASM1507037v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:21:59,393] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:21:59,395] [INFO] Found 6/6 markers.
[2024-01-24 13:21:59,437] [INFO] Query marker FASTA was written to GCF_015070375.1_ASM1507037v1_genomic.fna/markers.fasta
[2024-01-24 13:21:59,438] [INFO] Task started: Blastn
[2024-01-24 13:21:59,438] [INFO] Running command: blastn -query GCF_015070375.1_ASM1507037v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e7a8704-1dad-4afd-8d6c-565456a935a2/dqc_reference/reference_markers.fasta -out GCF_015070375.1_ASM1507037v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:00,837] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:00,842] [INFO] Selected 26 target genomes.
[2024-01-24 13:22:00,842] [INFO] Target genome list was writen to GCF_015070375.1_ASM1507037v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:00,853] [INFO] Task started: fastANI
[2024-01-24 13:22:00,854] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b59f691-8532-4b41-bd16-3118865feb63/GCF_015070375.1_ASM1507037v1_genomic.fna.gz --refList GCF_015070375.1_ASM1507037v1_genomic.fna/target_genomes.txt --output GCF_015070375.1_ASM1507037v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:31,669] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:31,669] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3e7a8704-1dad-4afd-8d6c-565456a935a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:31,670] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3e7a8704-1dad-4afd-8d6c-565456a935a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:31,691] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:22:31,691] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:31,692] [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
Nocardioides kribbensis	strain=DSM 16314	GCA_015070375.1	305517	305517	type	True	100.0	1365	1365	95	conclusive
Nocardioides marinisabuli	strain=DSM 18965	GCA_013466785.1	419476	419476	type	True	83.606	843	1365	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013409965.1	419476	419476	type	True	83.5019	853	1365	95	below_threshold
Nocardioides ginsengisegetis	strain=DSM 21349	GCA_014138045.1	661491	661491	type	True	82.3319	798	1365	95	below_threshold
Nocardioides lijunqiniae	strain=S-531	GCA_015024225.1	2760832	2760832	type	True	82.2427	796	1365	95	below_threshold
Nocardioides dongkuii	strain=S-713	GCA_014127485.1	2760089	2760089	type	True	82.2347	803	1365	95	below_threshold
Nocardioides marinus	strain=DSM 18248	GCA_013408145.1	374514	374514	type	True	82.2087	825	1365	95	below_threshold
Nocardioides deserti	strain=SC8A-24	GCA_014266025.1	1588644	1588644	type	True	82.1431	807	1365	95	below_threshold
Nocardioides deserti	strain=CGMCC 4.7183	GCA_014646035.1	1588644	1588644	type	True	82.1184	824	1365	95	below_threshold
Nocardioides luti	strain=KIGAM211	GCA_014212315.1	2761101	2761101	type	True	82.0887	812	1365	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_013409225.1	1045774	1045774	type	True	81.9325	891	1365	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_900101465.1	1045774	1045774	type	True	81.9042	894	1365	95	below_threshold
Nocardioides ungokensis	strain=LMG 28591	GCA_013466985.1	1643322	1643322	type	True	81.9035	791	1365	95	below_threshold
Nocardioides litoris	strain=DSM 103718	GCA_006346315.1	1926648	1926648	type	True	81.8733	854	1365	95	below_threshold
Nocardioides panaciterrulae	strain=DSM 21350	GCA_013409645.1	661492	661492	type	True	81.755	769	1365	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	81.1959	772	1365	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	81.1837	718	1365	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	80.6944	650	1365	95	below_threshold
Nocardioides humilatus	strain=BN130099	GCA_008373755.1	2607660	2607660	type	True	80.222	650	1365	95	below_threshold
Nocardioides carbamazepini	strain=CBZ_1	GCA_024614185.1	2854259	2854259	type	True	80.1397	719	1365	95	below_threshold
Nocardioides sambongensis	strain=KUDC 5002	GCA_006494815.1	2589074	2589074	type	True	80.0926	664	1365	95	below_threshold
Actinoplanes digitatis	strain=DSM 43149	GCA_014205335.1	1868	1868	type	True	76.3036	571	1365	95	below_threshold
Actinoplanes octamycinicus	strain=DSM 45809	GCA_014205225.1	135948	135948	type	True	76.2375	563	1365	95	below_threshold
Actinoplanes octamycinicus	strain=NBRC 14524	GCA_016862295.1	135948	135948	type	True	76.1645	557	1365	95	below_threshold
Actinoplanes ianthinogenes	strain=NBRC 13996	GCA_018324205.1	122358	122358	type	True	76.1435	530	1365	95	below_threshold
Allorhizocola rhizosphaerae	strain=CPCC 204380	GCA_003426775.1	1872709	1872709	type	True	76.0416	279	1365	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:31,693] [INFO] DFAST Taxonomy check result was written to GCF_015070375.1_ASM1507037v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:31,694] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:31,694] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:31,694] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3e7a8704-1dad-4afd-8d6c-565456a935a2/dqc_reference/checkm_data
[2024-01-24 13:22:31,695] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:31,738] [INFO] Task started: CheckM
[2024-01-24 13:22:31,738] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015070375.1_ASM1507037v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015070375.1_ASM1507037v1_genomic.fna/checkm_input GCF_015070375.1_ASM1507037v1_genomic.fna/checkm_result
[2024-01-24 13:23:34,465] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:34,467] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:34,490] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:34,491] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:34,491] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015070375.1_ASM1507037v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:34,492] [INFO] Task started: Blastn
[2024-01-24 13:23:34,492] [INFO] Running command: blastn -query GCF_015070375.1_ASM1507037v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e7a8704-1dad-4afd-8d6c-565456a935a2/dqc_reference/reference_markers_gtdb.fasta -out GCF_015070375.1_ASM1507037v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:36,708] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:36,713] [INFO] Selected 23 target genomes.
[2024-01-24 13:23:36,713] [INFO] Target genome list was writen to GCF_015070375.1_ASM1507037v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:36,751] [INFO] Task started: fastANI
[2024-01-24 13:23:36,752] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b59f691-8532-4b41-bd16-3118865feb63/GCF_015070375.1_ASM1507037v1_genomic.fna.gz --refList GCF_015070375.1_ASM1507037v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015070375.1_ASM1507037v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:24:03,467] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:03,489] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:24:03,489] [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_015070375.1	s__Nocardioides kribbensis	100.0	1365	1365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	97.79	97.79	0.94	0.92	3	conclusive
GCF_013466785.1	s__Nocardioides marinisabuli	83.6004	843	1365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_016907435.1	s__Nocardioides salarius	83.3114	864	1365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	3	-
GCF_001653335.1	s__Nocardioides dokdonensis	82.4569	842	1365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013177455.1	s__Nocardioides sp013177455	82.3535	836	1365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.28	98.92	0.97	0.95	4	-
GCF_014138045.1	s__Nocardioides ginsengisegetis	82.3204	799	1365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	96.18	96.18	0.84	0.84	2	-
GCF_013408145.1	s__Nocardioides marinus	82.1973	827	1365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	96.85	95.82	0.82	0.73	3	-
GCA_001627335.1	s__Nocardioides sp001627335	82.1836	724	1365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.38	96.50	0.91	0.88	12	-
GCF_011250565.1	s__Nocardioides sp011250565	82.1417	813	1365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014212315.1	s__Nocardioides luti	82.0835	812	1365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014266025.1	s__Nocardioides deserti	82.0508	817	1365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	0.99	0.99	2	-
GCF_002117935.1	s__Nocardioides sp002117935	82.0193	760	1365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	0.99	0.99	2	-
GCF_013155365.1	s__Nocardioides sp013155365	81.9871	754	1365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101465.1	s__Nocardioides lianchengensis	81.8884	895	1365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005954645.2	s__Nocardioides dongxiaopingii	81.7776	805	1365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.98	98.98	0.96	0.96	2	-
GCF_003710085.1	s__Nocardioides sp003710085	81.7547	767	1365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.05	99.05	0.97	0.97	2	-
GCF_013409645.1	s__Nocardioides panaciterrulae	81.7225	772	1365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425175.1	s__Nocardioides sp001425175	81.3897	802	1365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004137255.1	s__Nocardioides oleivorans	80.6493	760	1365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000284295.1	s__Actinoplanes missouriensis	76.2978	466	1365	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	76.2849	576	1365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000962825.1	s__Actinoplanes rectilineatus	76.2366	458	1365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003426775.1	s__Allorhizocola rhizosphaerae	76.0154	284	1365	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Allorhizocola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:24:03,491] [INFO] GTDB search result was written to GCF_015070375.1_ASM1507037v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:24:03,492] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:24:03,496] [INFO] DFAST_QC result json was written to GCF_015070375.1_ASM1507037v1_genomic.fna/dqc_result.json
[2024-01-24 13:24:03,496] [INFO] DFAST_QC completed!
[2024-01-24 13:24:03,497] [INFO] Total running time: 0h2m17s