[2024-01-24 13:40:33,104] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:33,108] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:33,108] [INFO] DQC Reference Directory: /var/lib/cwl/stg4a687d55-a50f-44fe-83c5-36b7feee478f/dqc_reference
[2024-01-24 13:40:34,409] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:34,414] [INFO] Task started: Prodigal
[2024-01-24 13:40:34,415] [INFO] Running command: gunzip -c /var/lib/cwl/stg076f3b7b-2082-434c-9088-b9978c062007/GCF_008704425.1_ASM870442v1_genomic.fna.gz | prodigal -d GCF_008704425.1_ASM870442v1_genomic.fna/cds.fna -a GCF_008704425.1_ASM870442v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:53,666] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:53,667] [INFO] Task started: HMMsearch
[2024-01-24 13:40:53,667] [INFO] Running command: hmmsearch --tblout GCF_008704425.1_ASM870442v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4a687d55-a50f-44fe-83c5-36b7feee478f/dqc_reference/reference_markers.hmm GCF_008704425.1_ASM870442v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:54,075] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:54,076] [INFO] Found 6/6 markers.
[2024-01-24 13:40:54,133] [INFO] Query marker FASTA was written to GCF_008704425.1_ASM870442v1_genomic.fna/markers.fasta
[2024-01-24 13:40:54,133] [INFO] Task started: Blastn
[2024-01-24 13:40:54,133] [INFO] Running command: blastn -query GCF_008704425.1_ASM870442v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a687d55-a50f-44fe-83c5-36b7feee478f/dqc_reference/reference_markers.fasta -out GCF_008704425.1_ASM870442v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:55,546] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:55,549] [INFO] Selected 15 target genomes.
[2024-01-24 13:40:55,549] [INFO] Target genome list was writen to GCF_008704425.1_ASM870442v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:55,557] [INFO] Task started: fastANI
[2024-01-24 13:40:55,557] [INFO] Running command: fastANI --query /var/lib/cwl/stg076f3b7b-2082-434c-9088-b9978c062007/GCF_008704425.1_ASM870442v1_genomic.fna.gz --refList GCF_008704425.1_ASM870442v1_genomic.fna/target_genomes.txt --output GCF_008704425.1_ASM870442v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:24,861] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:24,862] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4a687d55-a50f-44fe-83c5-36b7feee478f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:24,862] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4a687d55-a50f-44fe-83c5-36b7feee478f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:24,876] [INFO] Found 15 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:41:24,876] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:24,877] [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
Streptomyces fradiae	strain=ATCC 10745	GCA_008704425.1	1906	1906	suspected-type	True	100.0	2239	2241	95	conclusive
Streptomyces fradiae	strain=ATCC 10745	GCA_009834665.1	1906	1906	suspected-type	True	99.957	2168	2241	95	conclusive
Streptomyces fradiae	strain=DSM 40063	GCA_002119225.1	1906	1906	suspected-type	True	99.8731	1979	2241	95	conclusive
Streptomyces fradiae	strain=NRRL B-1195	GCA_002154445.1	1906	1906	suspected-type	True	99.3992	1283	2241	95	conclusive
Streptomyces roseolilacinus	strain=JCM 4335	GCA_014649335.1	66904	66904	type	True	89.1864	1682	2241	95	below_threshold
Streptomyces somaliensis	strain=DSM 40738	GCA_024349285.1	78355	78355	type	True	88.2571	1323	2241	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	88.1233	1366	2241	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	83.0055	1344	2241	95	below_threshold
Streptomyces nymphaeiformis	strain=SFB5A	GCA_014203895.1	2663842	2663842	type	True	82.7399	1357	2241	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	82.5966	1297	2241	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	81.4124	1294	2241	95	below_threshold
Actinacidiphila guanduensis	strain=CGMCC 4.2022	GCA_900103985.1	310781	310781	type	True	79.7654	1096	2241	95	below_threshold
Actinacidiphila paucisporea	strain=CGMCC 4.2025	GCA_900142575.1	310782	310782	type	True	79.7242	1065	2241	95	below_threshold
Wenjunlia vitaminophila	strain=DSM 41686	GCA_000380165.1	76728	76728	type	True	78.6357	856	2241	95	below_threshold
Wenjunlia vitaminophila	strain=ATCC 31673	GCA_001445835.1	76728	76728	type	True	78.6305	885	2241	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:24,878] [INFO] DFAST Taxonomy check result was written to GCF_008704425.1_ASM870442v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:24,879] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:24,879] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:24,879] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4a687d55-a50f-44fe-83c5-36b7feee478f/dqc_reference/checkm_data
[2024-01-24 13:41:24,881] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:24,947] [INFO] Task started: CheckM
[2024-01-24 13:41:24,947] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008704425.1_ASM870442v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008704425.1_ASM870442v1_genomic.fna/checkm_input GCF_008704425.1_ASM870442v1_genomic.fna/checkm_result
[2024-01-24 13:43:19,033] [INFO] Task succeeded: CheckM
[2024-01-24 13:43:19,035] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:43:19,056] [INFO] ===== Completeness check finished =====
[2024-01-24 13:43:19,057] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:43:19,057] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008704425.1_ASM870442v1_genomic.fna/markers.fasta)
[2024-01-24 13:43:19,058] [INFO] Task started: Blastn
[2024-01-24 13:43:19,058] [INFO] Running command: blastn -query GCF_008704425.1_ASM870442v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a687d55-a50f-44fe-83c5-36b7feee478f/dqc_reference/reference_markers_gtdb.fasta -out GCF_008704425.1_ASM870442v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:21,311] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:21,316] [INFO] Selected 12 target genomes.
[2024-01-24 13:43:21,316] [INFO] Target genome list was writen to GCF_008704425.1_ASM870442v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:43:21,372] [INFO] Task started: fastANI
[2024-01-24 13:43:21,373] [INFO] Running command: fastANI --query /var/lib/cwl/stg076f3b7b-2082-434c-9088-b9978c062007/GCF_008704425.1_ASM870442v1_genomic.fna.gz --refList GCF_008704425.1_ASM870442v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008704425.1_ASM870442v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:43:44,002] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:44,017] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:43:44,017] [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_008704425.1	s__Streptomyces fradiae	100.0	2237	2241	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.82	99.37	0.98	0.97	5	conclusive
GCF_000478605.2	s__Streptomyces thermolilacinus	89.7896	1733	2241	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649335.1	s__Streptomyces roseolilacinus	89.1676	1684	2241	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012396115.1	s__Streptomyces somaliensis	88.5647	1043	2241	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000258595.1	s__Streptomyces somaliensis_A	88.1049	1269	2241	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001484625.1	s__Streptomyces kanasensis	86.3938	1534	2241	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927245.1	s__Streptomyces sp012927245	82.8593	1350	2241	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014656075.1	s__Streptomyces hydrogenans	82.8588	1329	2241	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.17	97.53	0.88	0.87	3	-
GCF_013387495.1	s__Streptomyces sp013387495	82.5891	1254	2241	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103455.1	s__Streptomyces wuyuanensis	82.3235	1303	2241	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008042275.1	s__Streptomyces sp008042275	81.4614	1271	2241	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007595705.1	s__Streptomyces sp007595705	81.0071	1173	2241	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 13:43:44,019] [INFO] GTDB search result was written to GCF_008704425.1_ASM870442v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:43:44,019] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:43:44,023] [INFO] DFAST_QC result json was written to GCF_008704425.1_ASM870442v1_genomic.fna/dqc_result.json
[2024-01-24 13:43:44,023] [INFO] DFAST_QC completed!
[2024-01-24 13:43:44,023] [INFO] Total running time: 0h3m11s