[2024-01-24 15:02:07,440] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:07,443] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:07,443] [INFO] DQC Reference Directory: /var/lib/cwl/stg88afd208-43ce-4bfa-a49f-d8fcd88f4976/dqc_reference
[2024-01-24 15:02:09,610] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:09,613] [INFO] Task started: Prodigal
[2024-01-24 15:02:09,613] [INFO] Running command: gunzip -c /var/lib/cwl/stg23051f0e-ba73-4618-8f7e-a7f2fc5b1bbf/GCF_013409325.1_ASM1340932v1_genomic.fna.gz | prodigal -d GCF_013409325.1_ASM1340932v1_genomic.fna/cds.fna -a GCF_013409325.1_ASM1340932v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:24,709] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:24,709] [INFO] Task started: HMMsearch
[2024-01-24 15:02:24,709] [INFO] Running command: hmmsearch --tblout GCF_013409325.1_ASM1340932v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg88afd208-43ce-4bfa-a49f-d8fcd88f4976/dqc_reference/reference_markers.hmm GCF_013409325.1_ASM1340932v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:24,944] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:24,946] [INFO] Found 6/6 markers.
[2024-01-24 15:02:24,987] [INFO] Query marker FASTA was written to GCF_013409325.1_ASM1340932v1_genomic.fna/markers.fasta
[2024-01-24 15:02:24,987] [INFO] Task started: Blastn
[2024-01-24 15:02:24,988] [INFO] Running command: blastn -query GCF_013409325.1_ASM1340932v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg88afd208-43ce-4bfa-a49f-d8fcd88f4976/dqc_reference/reference_markers.fasta -out GCF_013409325.1_ASM1340932v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:26,176] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:26,179] [INFO] Selected 20 target genomes.
[2024-01-24 15:02:26,180] [INFO] Target genome list was writen to GCF_013409325.1_ASM1340932v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:26,190] [INFO] Task started: fastANI
[2024-01-24 15:02:26,190] [INFO] Running command: fastANI --query /var/lib/cwl/stg23051f0e-ba73-4618-8f7e-a7f2fc5b1bbf/GCF_013409325.1_ASM1340932v1_genomic.fna.gz --refList GCF_013409325.1_ASM1340932v1_genomic.fna/target_genomes.txt --output GCF_013409325.1_ASM1340932v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:02:42,853] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:42,853] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg88afd208-43ce-4bfa-a49f-d8fcd88f4976/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:02:42,854] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg88afd208-43ce-4bfa-a49f-d8fcd88f4976/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:02:42,872] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:02:42,872] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:02:42,872] [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
Kineosphaera limosa	strain=DSM 14548	GCA_013409325.1	111564	111564	type	True	100.0	1648	1648	95	conclusive
Kineosphaera limosa	strain=NBRC 100340	GCA_000298215.1	111564	111564	type	True	99.9024	1527	1648	95	conclusive
Mobilicoccus massiliensis	strain=SIT2	GCA_000826525.2	1522310	1522310	type	True	79.182	527	1648	95	below_threshold
Mobilicoccus pelagius	strain=NBRC 104925	GCA_000247995.2	746032	746032	type	True	78.8958	488	1648	95	below_threshold
Arsenicicoccus bolidensis	strain=DSM 15745	GCA_000426385.1	229480	229480	type	True	78.7021	435	1648	95	below_threshold
Arsenicicoccus cauae	strain=MKL-02	GCA_009707125.1	2663847	2663847	type	True	78.6916	412	1648	95	below_threshold
Barrientosiimonas humi	strain=DSM 24617	GCA_006716095.1	999931	999931	type	True	78.6731	440	1648	95	below_threshold
Barrientosiimonas humi	strain=type strain: 39	GCA_910573815.1	999931	999931	type	True	78.6558	433	1648	95	below_threshold
Pedococcus cremeus	strain=CGMCC 1.6963	GCA_900111375.1	587636	587636	type	True	78.641	448	1648	95	below_threshold
Arsenicicoccus piscis	strain=DSM 22760	GCA_022568835.1	673954	673954	type	True	78.6393	424	1648	95	below_threshold
Knoellia flava	strain=TL1	GCA_000768675.1	913969	913969	type	True	78.448	391	1648	95	below_threshold
Janibacter terrae	strain=NBRC 107853	GCA_001591405.1	103817	103817	type	True	78.4332	401	1648	95	below_threshold
Knoellia flava	strain=CGMCC 1.10749	GCA_014636255.1	913969	913969	type	True	78.3774	412	1648	95	below_threshold
Arsenicicoccus dermatophilus	strain=DSM 25571	GCA_022568795.1	1076331	1076331	type	True	78.2891	394	1648	95	below_threshold
Janibacter indicus	strain=CGMCC 1.12511	GCA_900176385.1	857417	857417	type	True	78.2579	400	1648	95	below_threshold
Phycicoccus jejuensis	strain=NRRL B-24460	GCA_000720925.1	367299	367299	type	True	78.2442	460	1648	95	below_threshold
Luteipulveratus halotolerans	strain=C296001	GCA_001247745.1	1631356	1631356	type	True	78.2182	405	1648	95	below_threshold
Flexivirga aerilata	strain=ID2601S	GCA_013002715.1	1656889	1656889	type	True	78.1066	388	1648	95	below_threshold
Phycicoccus flavus	strain=CMS6Z-2	GCA_004025965.2	2502783	2502783	type	True	78.017	446	1648	95	below_threshold
Janibacter melonis	strain=NBRC107855	GCA_020567375.1	262209	262209	type	True	77.9797	426	1648	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:02:42,874] [INFO] DFAST Taxonomy check result was written to GCF_013409325.1_ASM1340932v1_genomic.fna/tc_result.tsv
[2024-01-24 15:02:42,874] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:02:42,875] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:02:42,875] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg88afd208-43ce-4bfa-a49f-d8fcd88f4976/dqc_reference/checkm_data
[2024-01-24 15:02:42,876] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:02:42,937] [INFO] Task started: CheckM
[2024-01-24 15:02:42,937] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013409325.1_ASM1340932v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013409325.1_ASM1340932v1_genomic.fna/checkm_input GCF_013409325.1_ASM1340932v1_genomic.fna/checkm_result
[2024-01-24 15:03:38,626] [INFO] Task succeeded: CheckM
[2024-01-24 15:03:38,627] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:03:38,647] [INFO] ===== Completeness check finished =====
[2024-01-24 15:03:38,648] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:03:38,648] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013409325.1_ASM1340932v1_genomic.fna/markers.fasta)
[2024-01-24 15:03:38,648] [INFO] Task started: Blastn
[2024-01-24 15:03:38,648] [INFO] Running command: blastn -query GCF_013409325.1_ASM1340932v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg88afd208-43ce-4bfa-a49f-d8fcd88f4976/dqc_reference/reference_markers_gtdb.fasta -out GCF_013409325.1_ASM1340932v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:40,598] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:40,601] [INFO] Selected 16 target genomes.
[2024-01-24 15:03:40,602] [INFO] Target genome list was writen to GCF_013409325.1_ASM1340932v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:03:40,616] [INFO] Task started: fastANI
[2024-01-24 15:03:40,616] [INFO] Running command: fastANI --query /var/lib/cwl/stg23051f0e-ba73-4618-8f7e-a7f2fc5b1bbf/GCF_013409325.1_ASM1340932v1_genomic.fna.gz --refList GCF_013409325.1_ASM1340932v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013409325.1_ASM1340932v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:03:54,481] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:54,494] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:03:54,495] [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_000298215.1	s__Kineosphaera limosa	99.9024	1527	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Kineosphaera	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_001515525.1	s__Piscicoccus intestinalis	81.7545	836	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Piscicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000826525.2	s__Mobilicoccus massiliensis	79.1462	533	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Mobilicoccus	95.0	100.00	100.00	0.99	0.99	2	-
GCA_014857905.1	s__JACYXE01 sp014857905	79.1451	648	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__JACYXE01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000247995.1	s__Mobilicoccus pelagius	78.9007	488	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Mobilicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716205.1	s__Oryzihumus leptocrescens	78.8523	448	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Oryzihumus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716095.1	s__Barrientosiimonas humi	78.7312	434	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Barrientosiimonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001189535.1	s__Arsenicicoccus sp001189535	78.7056	449	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Arsenicicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013041615.1	s__Pedococcus sp013041615	78.5499	405	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016699675.1	s__Austwickia sp016699675	78.4983	481	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Austwickia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552435.1	s__Kribbia dieselivorans	78.4769	290	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Kribbia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001247745.1	s__Luteipulveratus halotolerans	78.2554	401	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Luteipulveratus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720925.1	s__Phycicoccus jejuensis	78.251	459	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	96.36	95.39	0.88	0.87	4	-
GCF_016887965.1	s__Phycicoccus sp016887965	78.0277	476	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715055.1	s__Lapillicoccus jejuensis	77.9963	493	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Lapillicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001956915.1	s__Monashia flava	77.978	441	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Monashia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:03:54,496] [INFO] GTDB search result was written to GCF_013409325.1_ASM1340932v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:03:54,497] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:03:54,501] [INFO] DFAST_QC result json was written to GCF_013409325.1_ASM1340932v1_genomic.fna/dqc_result.json
[2024-01-24 15:03:54,502] [INFO] DFAST_QC completed!
[2024-01-24 15:03:54,502] [INFO] Total running time: 0h1m47s