[2024-01-25 19:44:20,788] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:44:20,789] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:44:20,789] [INFO] DQC Reference Directory: /var/lib/cwl/stg1c2c7fc6-af4b-4e21-b210-9959a0936706/dqc_reference
[2024-01-25 19:44:21,917] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:44:21,918] [INFO] Task started: Prodigal
[2024-01-25 19:44:21,918] [INFO] Running command: gunzip -c /var/lib/cwl/stg3ebe0ca5-ab64-41ad-9b07-b74db2182301/GCF_021246445.1_ASM2124644v1_genomic.fna.gz | prodigal -d GCF_021246445.1_ASM2124644v1_genomic.fna/cds.fna -a GCF_021246445.1_ASM2124644v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:44:32,633] [INFO] Task succeeded: Prodigal
[2024-01-25 19:44:32,633] [INFO] Task started: HMMsearch
[2024-01-25 19:44:32,633] [INFO] Running command: hmmsearch --tblout GCF_021246445.1_ASM2124644v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1c2c7fc6-af4b-4e21-b210-9959a0936706/dqc_reference/reference_markers.hmm GCF_021246445.1_ASM2124644v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:44:32,836] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:44:32,837] [INFO] Found 6/6 markers.
[2024-01-25 19:44:32,868] [INFO] Query marker FASTA was written to GCF_021246445.1_ASM2124644v1_genomic.fna/markers.fasta
[2024-01-25 19:44:32,869] [INFO] Task started: Blastn
[2024-01-25 19:44:32,869] [INFO] Running command: blastn -query GCF_021246445.1_ASM2124644v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c2c7fc6-af4b-4e21-b210-9959a0936706/dqc_reference/reference_markers.fasta -out GCF_021246445.1_ASM2124644v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:44:33,704] [INFO] Task succeeded: Blastn
[2024-01-25 19:44:33,707] [INFO] Selected 13 target genomes.
[2024-01-25 19:44:33,707] [INFO] Target genome list was writen to GCF_021246445.1_ASM2124644v1_genomic.fna/target_genomes.txt
[2024-01-25 19:44:33,718] [INFO] Task started: fastANI
[2024-01-25 19:44:33,718] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ebe0ca5-ab64-41ad-9b07-b74db2182301/GCF_021246445.1_ASM2124644v1_genomic.fna.gz --refList GCF_021246445.1_ASM2124644v1_genomic.fna/target_genomes.txt --output GCF_021246445.1_ASM2124644v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:44:45,215] [INFO] Task succeeded: fastANI
[2024-01-25 19:44:45,216] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1c2c7fc6-af4b-4e21-b210-9959a0936706/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:44:45,216] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1c2c7fc6-af4b-4e21-b210-9959a0936706/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:44:45,224] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:44:45,224] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:44:45,224] [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
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	100.0	1298	1299	95	conclusive
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	78.0716	399	1299	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	77.9406	443	1299	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	76.7925	280	1299	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	76.4579	375	1299	95	below_threshold
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	76.31	250	1299	95	below_threshold
Lysobacter avium	strain=H23M41	GCA_015209745.1	2781023	2781023	type	True	75.4532	51	1299	95	below_threshold
Lysobacter ciconiae	strain=H21R20	GCA_015209725.1	2781022	2781022	type	True	75.414	56	1299	95	below_threshold
Nocardiopsis prasina	strain=DSM 43845	GCA_000341265.1	2015	2015	type	True	75.3393	201	1299	95	below_threshold
Actinoplanes lichenicola	strain=LDG1-01	GCA_016785085.1	2802976	2802976	type	True	75.2193	322	1299	95	below_threshold
Actinoplanes brasiliensis	strain=NBRC 13938	GCA_016862015.1	52695	52695	type	True	75.2123	292	1299	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:44:45,226] [INFO] DFAST Taxonomy check result was written to GCF_021246445.1_ASM2124644v1_genomic.fna/tc_result.tsv
[2024-01-25 19:44:45,226] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:44:45,226] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:44:45,226] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1c2c7fc6-af4b-4e21-b210-9959a0936706/dqc_reference/checkm_data
[2024-01-25 19:44:45,227] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:44:45,266] [INFO] Task started: CheckM
[2024-01-25 19:44:45,266] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021246445.1_ASM2124644v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021246445.1_ASM2124644v1_genomic.fna/checkm_input GCF_021246445.1_ASM2124644v1_genomic.fna/checkm_result
[2024-01-25 19:46:20,881] [INFO] Task succeeded: CheckM
[2024-01-25 19:46:20,882] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-25 19:46:20,909] [INFO] ===== Completeness check finished =====
[2024-01-25 19:46:20,909] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:46:20,910] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021246445.1_ASM2124644v1_genomic.fna/markers.fasta)
[2024-01-25 19:46:20,910] [INFO] Task started: Blastn
[2024-01-25 19:46:20,910] [INFO] Running command: blastn -query GCF_021246445.1_ASM2124644v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c2c7fc6-af4b-4e21-b210-9959a0936706/dqc_reference/reference_markers_gtdb.fasta -out GCF_021246445.1_ASM2124644v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:46:22,272] [INFO] Task succeeded: Blastn
[2024-01-25 19:46:22,275] [INFO] Selected 18 target genomes.
[2024-01-25 19:46:22,275] [INFO] Target genome list was writen to GCF_021246445.1_ASM2124644v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:46:22,296] [INFO] Task started: fastANI
[2024-01-25 19:46:22,296] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ebe0ca5-ab64-41ad-9b07-b74db2182301/GCF_021246445.1_ASM2124644v1_genomic.fna.gz --refList GCF_021246445.1_ASM2124644v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021246445.1_ASM2124644v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:46:33,751] [INFO] Task succeeded: fastANI
[2024-01-25 19:46:33,762] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:46:33,763] [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
GCA_018969405.1	s__F1-20-MAGs160 sp018969405	79.9777	412	1299	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_018882825.1	s__F1-20-MAGs160 sp018882825	78.9084	296	1299	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_016649895.1	s__Actinomarinicola sp016649895	78.2528	353	1299	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SKKL01;g__Actinomarinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794585.1	s__JAEUJM01 sp016794585	78.1643	526	1299	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAEUJM01;g__JAEUJM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014805525.1	s__Rhabdothermincola sediminis	78.0889	397	1299	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8139;g__Rhabdothermincola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007121465.1	s__SKKL01 sp007121465	78.0464	314	1299	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SKKL01;g__SKKL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002403895.1	s__UBA4742 sp002403895	77.9866	318	1299	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8139;g__UBA4742	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009650215.1	s__Actinomarinicola tropica	77.9714	439	1299	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SKKL01;g__Actinomarinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009705225.1	s__F1-20-MAGs160 sp009705225	77.8571	253	1299	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8139;g__F1-20-MAGs160	95.0	99.41	99.41	0.86	0.86	2	-
GCA_009703925.1	s__F1-20-MAGs160 sp009703925	77.7789	251	1299	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	-
GCF_019048865.1	s__Aquihabitans sp019048865	77.7739	532	1299	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__Aquihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004366205.1	s__SIRW01 sp004366205	77.4678	400	1299	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SIRW01;g__SIRW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017577565.1	s__ZC4RG19 sp017577565	77.4629	440	1299	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JACDCH01;g__ZC4RG19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016185275.1	s__JACPNX01 sp016185275	77.3058	362	1299	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JACPNX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012730075.1	s__JAAYBP01 sp012730075	77.0906	314	1299	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JAAYBP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805655.1	s__CADCTF01 sp902805655	77.0096	259	1299	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__CADCTF01;g__CADCTF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009785715.1	s__WQVT01 sp009785715	76.6061	110	1299	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Palsa-688;g__WQVT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003157945.1	s__Bog-756 sp003157945	75.9463	173	1299	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Bog-756	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:46:33,764] [INFO] GTDB search result was written to GCF_021246445.1_ASM2124644v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:46:33,765] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:46:33,768] [INFO] DFAST_QC result json was written to GCF_021246445.1_ASM2124644v1_genomic.fna/dqc_result.json
[2024-01-25 19:46:33,768] [INFO] DFAST_QC completed!
[2024-01-25 19:46:33,768] [INFO] Total running time: 0h2m13s