[2024-01-25 20:12:05,368] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:12:05,370] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:12:05,370] [INFO] DQC Reference Directory: /var/lib/cwl/stge3ff737d-7ea5-4d37-b3c6-453c96510b2c/dqc_reference
[2024-01-25 20:12:06,600] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:12:06,600] [INFO] Task started: Prodigal
[2024-01-25 20:12:06,600] [INFO] Running command: gunzip -c /var/lib/cwl/stg1bbb9bab-a401-4a54-9f3a-cea7845702d8/GCF_009650215.1_ASM965021v1_genomic.fna.gz | prodigal -d GCF_009650215.1_ASM965021v1_genomic.fna/cds.fna -a GCF_009650215.1_ASM965021v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:12:15,930] [INFO] Task succeeded: Prodigal
[2024-01-25 20:12:15,930] [INFO] Task started: HMMsearch
[2024-01-25 20:12:15,930] [INFO] Running command: hmmsearch --tblout GCF_009650215.1_ASM965021v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge3ff737d-7ea5-4d37-b3c6-453c96510b2c/dqc_reference/reference_markers.hmm GCF_009650215.1_ASM965021v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:12:16,150] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:12:16,152] [INFO] Found 6/6 markers.
[2024-01-25 20:12:16,181] [INFO] Query marker FASTA was written to GCF_009650215.1_ASM965021v1_genomic.fna/markers.fasta
[2024-01-25 20:12:16,181] [INFO] Task started: Blastn
[2024-01-25 20:12:16,182] [INFO] Running command: blastn -query GCF_009650215.1_ASM965021v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge3ff737d-7ea5-4d37-b3c6-453c96510b2c/dqc_reference/reference_markers.fasta -out GCF_009650215.1_ASM965021v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:12:17,103] [INFO] Task succeeded: Blastn
[2024-01-25 20:12:17,106] [INFO] Selected 21 target genomes.
[2024-01-25 20:12:17,106] [INFO] Target genome list was writen to GCF_009650215.1_ASM965021v1_genomic.fna/target_genomes.txt
[2024-01-25 20:12:17,127] [INFO] Task started: fastANI
[2024-01-25 20:12:17,128] [INFO] Running command: fastANI --query /var/lib/cwl/stg1bbb9bab-a401-4a54-9f3a-cea7845702d8/GCF_009650215.1_ASM965021v1_genomic.fna.gz --refList GCF_009650215.1_ASM965021v1_genomic.fna/target_genomes.txt --output GCF_009650215.1_ASM965021v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:12:34,899] [INFO] Task succeeded: fastANI
[2024-01-25 20:12:34,900] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge3ff737d-7ea5-4d37-b3c6-453c96510b2c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:12:34,900] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge3ff737d-7ea5-4d37-b3c6-453c96510b2c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:12:34,925] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:12:34,926] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:12:34,926] [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
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	100.0	1238	1238	95	conclusive
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	78.0735	428	1238	95	below_threshold
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	77.5379	314	1238	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	76.6717	333	1238	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	76.5561	400	1238	95	below_threshold
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	76.185	298	1238	95	below_threshold
Motilibacter peucedani	strain=RP-AC37	GCA_003634695.1	598650	598650	type	True	75.716	307	1238	95	below_threshold
Nocardioides perillae	strain=DSM 24552	GCA_013409425.1	1119534	1119534	type	True	75.6507	333	1238	95	below_threshold
Nocardioides allogilvus	strain=KCTC 49020	GCA_003047285.1	2072017	2072017	type	True	75.6374	235	1238	95	below_threshold
Sphaerimonospora thailandensis	strain=NBRC 107569	GCA_016863115.1	795644	795644	type	True	75.6162	199	1238	95	below_threshold
Nocardioides humilatus	strain=BN130099	GCA_008373755.1	2607660	2607660	type	True	75.5595	241	1238	95	below_threshold
Streptomonospora litoralis	strain=M2	GCA_004323735.1	2498135	2498135	type	True	75.4185	238	1238	95	below_threshold
Bifidobacterium avesanii	strain=DSM 100685	GCA_009299475.1	1798157	1798157	type	True	75.4044	80	1238	95	below_threshold
Bifidobacterium avesanii	strain=TREC	GCA_010667745.1	1798157	1798157	type	True	75.3928	81	1238	95	below_threshold
Serinicoccus kebangsaanensis	strain=P2D13-UKM	GCA_008919445.1	2602069	2602069	type	True	75.3568	175	1238	95	below_threshold
Asanoa ishikariensis	strain=NBRC 14551	GCA_016862535.1	137265	137265	type	True	75.2579	307	1238	95	below_threshold
Asanoa ishikariensis	strain=DSM 44718	GCA_900107455.1	137265	137265	type	True	75.2579	315	1238	95	below_threshold
Baekduia soli	strain=BR7-21	GCA_007970665.1	496014	496014	type	True	75.2304	330	1238	95	below_threshold
Catellatospora paridis	strain=NEAU-CL2	GCA_009720365.1	1617086	1617086	type	True	75.2116	288	1238	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	75.1812	164	1238	95	below_threshold
Catellatospora citrea	strain=NBRC 14495	GCA_016862615.1	53366	53366	type	True	75.074	329	1238	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:12:34,933] [INFO] DFAST Taxonomy check result was written to GCF_009650215.1_ASM965021v1_genomic.fna/tc_result.tsv
[2024-01-25 20:12:34,933] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:12:34,934] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:12:34,934] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge3ff737d-7ea5-4d37-b3c6-453c96510b2c/dqc_reference/checkm_data
[2024-01-25 20:12:34,935] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:12:34,972] [INFO] Task started: CheckM
[2024-01-25 20:12:34,973] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009650215.1_ASM965021v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009650215.1_ASM965021v1_genomic.fna/checkm_input GCF_009650215.1_ASM965021v1_genomic.fna/checkm_result
[2024-01-25 20:13:52,748] [INFO] Task succeeded: CheckM
[2024-01-25 20:13:52,749] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:13:52,770] [INFO] ===== Completeness check finished =====
[2024-01-25 20:13:52,770] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:13:52,771] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009650215.1_ASM965021v1_genomic.fna/markers.fasta)
[2024-01-25 20:13:52,771] [INFO] Task started: Blastn
[2024-01-25 20:13:52,771] [INFO] Running command: blastn -query GCF_009650215.1_ASM965021v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge3ff737d-7ea5-4d37-b3c6-453c96510b2c/dqc_reference/reference_markers_gtdb.fasta -out GCF_009650215.1_ASM965021v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:13:54,481] [INFO] Task succeeded: Blastn
[2024-01-25 20:13:54,484] [INFO] Selected 16 target genomes.
[2024-01-25 20:13:54,484] [INFO] Target genome list was writen to GCF_009650215.1_ASM965021v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:13:54,493] [INFO] Task started: fastANI
[2024-01-25 20:13:54,493] [INFO] Running command: fastANI --query /var/lib/cwl/stg1bbb9bab-a401-4a54-9f3a-cea7845702d8/GCF_009650215.1_ASM965021v1_genomic.fna.gz --refList GCF_009650215.1_ASM965021v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009650215.1_ASM965021v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:14:05,701] [INFO] Task succeeded: fastANI
[2024-01-25 20:14:05,712] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:14:05,712] [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_009650215.1	s__Actinomarinicola tropica	100.0	1238	1238	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SKKL01;g__Actinomarinicola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016649895.1	s__Actinomarinicola sp016649895	81.2658	641	1238	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SKKL01;g__Actinomarinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007121465.1	s__SKKL01 sp007121465	79.5352	449	1238	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SKKL01;g__SKKL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004366205.1	s__SIRW01 sp004366205	77.9978	428	1238	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SIRW01;g__SIRW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794585.1	s__JAEUJM01 sp016794585	77.9474	484	1238	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAEUJM01;g__JAEUJM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017882935.1	s__JADGOP01 sp017882935	77.8637	270	1238	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JADGOP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019048865.1	s__Aquihabitans sp019048865	77.7096	510	1238	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__Aquihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805555.1	s__CADCSY01 sp902805555	77.4871	346	1238	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__CADCSY01;g__CADCSY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009703925.1	s__F1-20-MAGs160 sp009703925	77.471	128	1238	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8139;g__F1-20-MAGs160	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012730075.1	s__JAAYBP01 sp012730075	77.4665	364	1238	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JAAYBP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016185305.1	s__JACPNV01 sp016185305	77.3846	224	1238	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8139;g__JACPNV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003962875.1	s__AWTP1-35 sp003962875	77.3384	279	1238	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__AWTP1-35	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005888325.1	s__AC-14 sp005888325	77.2511	302	1238	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__AC-14;g__AC-14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268735.1	s__AWTP1-35 sp018268735	77.1	184	1238	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__AWTP1-35	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903873135.1	s__SXMI01 sp903873135	77.0072	284	1238	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__SXMI01	95.0	99.54	99.49	0.91	0.89	9	-
GCA_903868545.1	s__CAIPVR01 sp903868545	76.9866	328	1238	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__CAIPVR01	95.0	99.51	99.50	0.87	0.86	3	-
--------------------------------------------------------------------------------
[2024-01-25 20:14:05,714] [INFO] GTDB search result was written to GCF_009650215.1_ASM965021v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:14:05,714] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:14:05,718] [INFO] DFAST_QC result json was written to GCF_009650215.1_ASM965021v1_genomic.fna/dqc_result.json
[2024-01-25 20:14:05,718] [INFO] DFAST_QC completed!
[2024-01-25 20:14:05,718] [INFO] Total running time: 0h2m0s