[2024-01-24 14:14:32,003] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:32,005] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:32,005] [INFO] DQC Reference Directory: /var/lib/cwl/stgde518526-f108-46b4-9cad-bb8f4d7aa570/dqc_reference
[2024-01-24 14:14:33,257] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:33,258] [INFO] Task started: Prodigal
[2024-01-24 14:14:33,258] [INFO] Running command: gunzip -c /var/lib/cwl/stgb035b282-4b50-48f8-becf-7f98f0a91fe0/GCF_014205315.1_ASM1420531v1_genomic.fna.gz | prodigal -d GCF_014205315.1_ASM1420531v1_genomic.fna/cds.fna -a GCF_014205315.1_ASM1420531v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:17:02,794] [INFO] Task succeeded: Prodigal
[2024-01-24 14:17:02,795] [INFO] Task started: HMMsearch
[2024-01-24 14:17:02,795] [INFO] Running command: hmmsearch --tblout GCF_014205315.1_ASM1420531v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgde518526-f108-46b4-9cad-bb8f4d7aa570/dqc_reference/reference_markers.hmm GCF_014205315.1_ASM1420531v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:17:03,392] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:17:03,393] [INFO] Found 6/6 markers.
[2024-01-24 14:17:03,486] [INFO] Query marker FASTA was written to GCF_014205315.1_ASM1420531v1_genomic.fna/markers.fasta
[2024-01-24 14:17:03,487] [INFO] Task started: Blastn
[2024-01-24 14:17:03,487] [INFO] Running command: blastn -query GCF_014205315.1_ASM1420531v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde518526-f108-46b4-9cad-bb8f4d7aa570/dqc_reference/reference_markers.fasta -out GCF_014205315.1_ASM1420531v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:17:04,893] [INFO] Task succeeded: Blastn
[2024-01-24 14:17:04,897] [INFO] Selected 10 target genomes.
[2024-01-24 14:17:04,898] [INFO] Target genome list was writen to GCF_014205315.1_ASM1420531v1_genomic.fna/target_genomes.txt
[2024-01-24 14:17:04,905] [INFO] Task started: fastANI
[2024-01-24 14:17:04,906] [INFO] Running command: fastANI --query /var/lib/cwl/stgb035b282-4b50-48f8-becf-7f98f0a91fe0/GCF_014205315.1_ASM1420531v1_genomic.fna.gz --refList GCF_014205315.1_ASM1420531v1_genomic.fna/target_genomes.txt --output GCF_014205315.1_ASM1420531v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:17:48,042] [INFO] Task succeeded: fastANI
[2024-01-24 14:17:48,042] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgde518526-f108-46b4-9cad-bb8f4d7aa570/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:17:48,043] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgde518526-f108-46b4-9cad-bb8f4d7aa570/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:17:48,052] [INFO] Found 10 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 14:17:48,052] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:17:48,052] [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 rapamycinicus	strain=DSM 41530	GCA_014205315.1	1226757	1226757	type	True	100.0	4201	4207	95	inconclusive
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_003675955.1	1226757	1226757	type	True	99.9957	4188	4207	95	inconclusive
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_024298965.1	1226757	1226757	type	True	99.9876	4132	4207	95	inconclusive
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_000418455.1	1226757	1226757	type	True	99.9004	4152	4207	95	inconclusive
Streptomyces iranensis	strain=DSM 41954	GCA_017874715.1	576784	576784	type	True	95.6347	3227	4207	95	inconclusive
Streptomyces javensis	strain=DSM 41764	GCA_016103505.1	114698	114698	type	True	94.4828	2354	4207	95	below_threshold
Streptomyces albireticuli	strain=NRRL B1670	GCA_021228125.1	1940	1940	type	True	81.0037	1457	4207	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=R7	GCA_022760195.1	132474	1927	type	True	80.9242	1590	4207	95	below_threshold
Streptomyces paromomycinus	strain=NBRC 15454	GCA_003865155.1	92743	92743	type	True	80.8526	1625	4207	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	80.4083	1329	4207	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:17:48,054] [INFO] DFAST Taxonomy check result was written to GCF_014205315.1_ASM1420531v1_genomic.fna/tc_result.tsv
[2024-01-24 14:17:48,055] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:17:48,055] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:17:48,055] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgde518526-f108-46b4-9cad-bb8f4d7aa570/dqc_reference/checkm_data
[2024-01-24 14:17:48,056] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:17:48,169] [INFO] Task started: CheckM
[2024-01-24 14:17:48,169] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014205315.1_ASM1420531v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014205315.1_ASM1420531v1_genomic.fna/checkm_input GCF_014205315.1_ASM1420531v1_genomic.fna/checkm_result
[2024-01-24 14:25:42,474] [INFO] Task succeeded: CheckM
[2024-01-24 14:25:42,477] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:25:42,500] [INFO] ===== Completeness check finished =====
[2024-01-24 14:25:42,500] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:25:42,502] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014205315.1_ASM1420531v1_genomic.fna/markers.fasta)
[2024-01-24 14:25:42,502] [INFO] Task started: Blastn
[2024-01-24 14:25:42,502] [INFO] Running command: blastn -query GCF_014205315.1_ASM1420531v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde518526-f108-46b4-9cad-bb8f4d7aa570/dqc_reference/reference_markers_gtdb.fasta -out GCF_014205315.1_ASM1420531v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:25:44,635] [INFO] Task succeeded: Blastn
[2024-01-24 14:25:44,638] [INFO] Selected 6 target genomes.
[2024-01-24 14:25:44,638] [INFO] Target genome list was writen to GCF_014205315.1_ASM1420531v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:25:44,652] [INFO] Task started: fastANI
[2024-01-24 14:25:44,653] [INFO] Running command: fastANI --query /var/lib/cwl/stgb035b282-4b50-48f8-becf-7f98f0a91fe0/GCF_014205315.1_ASM1420531v1_genomic.fna.gz --refList GCF_014205315.1_ASM1420531v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014205315.1_ASM1420531v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:26:19,076] [INFO] Task succeeded: fastANI
[2024-01-24 14:26:19,089] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:26:19,089] [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_003675955.1	s__Streptomyces rapamycinicus	99.9957	4188	4207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.67	99.95	99.91	0.99	0.99	3	conclusive
GCF_017874715.1	s__Streptomyces iranensis	95.6243	3229	4207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.67	99.98	99.98	1.00	1.00	2	-
GCF_016741935.1	s__Streptomyces sp016741935	94.9107	3161	4207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0488	N/A	N/A	N/A	N/A	1	-
GCF_018138715.1	s__Streptomyces asiaticus	94.6952	3171	4207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.17	95.36	0.90	0.81	10	-
GCA_005405945.1	s__Streptomyces violaceusniger	94.1343	3100	4207	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.67	97.67	0.85	0.85	2	-
GCF_000968685.2	s__Streptomyces antioxidans	93.4995	2502	4207	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 14:26:19,091] [INFO] GTDB search result was written to GCF_014205315.1_ASM1420531v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:26:19,092] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:26:19,096] [INFO] DFAST_QC result json was written to GCF_014205315.1_ASM1420531v1_genomic.fna/dqc_result.json
[2024-01-24 14:26:19,096] [INFO] DFAST_QC completed!
[2024-01-24 14:26:19,096] [INFO] Total running time: 0h11m47s