[2024-01-24 13:22:25,587] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:25,588] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:25,589] [INFO] DQC Reference Directory: /var/lib/cwl/stgdff510e5-3598-4e39-a0f0-ba8fdaac444b/dqc_reference
[2024-01-24 13:22:26,765] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:26,766] [INFO] Task started: Prodigal
[2024-01-24 13:22:26,766] [INFO] Running command: gunzip -c /var/lib/cwl/stg0a347ab8-f44f-45ad-9215-5050e72a1d1e/GCF_014648775.1_ASM1464877v1_genomic.fna.gz | prodigal -d GCF_014648775.1_ASM1464877v1_genomic.fna/cds.fna -a GCF_014648775.1_ASM1464877v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:47,630] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:47,630] [INFO] Task started: HMMsearch
[2024-01-24 13:22:47,631] [INFO] Running command: hmmsearch --tblout GCF_014648775.1_ASM1464877v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdff510e5-3598-4e39-a0f0-ba8fdaac444b/dqc_reference/reference_markers.hmm GCF_014648775.1_ASM1464877v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:47,962] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:47,964] [INFO] Found 6/6 markers.
[2024-01-24 13:22:48,021] [INFO] Query marker FASTA was written to GCF_014648775.1_ASM1464877v1_genomic.fna/markers.fasta
[2024-01-24 13:22:48,021] [INFO] Task started: Blastn
[2024-01-24 13:22:48,022] [INFO] Running command: blastn -query GCF_014648775.1_ASM1464877v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdff510e5-3598-4e39-a0f0-ba8fdaac444b/dqc_reference/reference_markers.fasta -out GCF_014648775.1_ASM1464877v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:49,373] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:49,377] [INFO] Selected 14 target genomes.
[2024-01-24 13:22:49,378] [INFO] Target genome list was writen to GCF_014648775.1_ASM1464877v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:49,506] [INFO] Task started: fastANI
[2024-01-24 13:22:49,506] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a347ab8-f44f-45ad-9215-5050e72a1d1e/GCF_014648775.1_ASM1464877v1_genomic.fna.gz --refList GCF_014648775.1_ASM1464877v1_genomic.fna/target_genomes.txt --output GCF_014648775.1_ASM1464877v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:23:16,064] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:16,065] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdff510e5-3598-4e39-a0f0-ba8fdaac444b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:23:16,065] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdff510e5-3598-4e39-a0f0-ba8fdaac444b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:23:16,079] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:23:16,079] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:23:16,079] [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 abikoensis	strain=JCM 4002	GCA_014648775.1	97398	97398	type	True	100.0	2316	2317	95	conclusive
Streptomyces griseocarneus	strain=CGMCC4.1088	GCA_020093395.1	51201	51201	type	True	86.7775	1564	2317	95	below_threshold
Streptomyces griseocarneus	strain=JCM 4580	GCA_014655595.1	51201	51201	type	True	86.712	1578	2317	95	below_threshold
Streptomyces olivoverticillatus	strain=CECT 3266	GCA_014203555.1	66427	66427	type	True	86.3936	1403	2317	95	below_threshold
Streptomyces mashuensis	strain=JCM 4059	GCA_014654785.1	33904	33904	type	True	85.0861	1526	2317	95	below_threshold
Streptomyces morookaense	strain=DSM 40503	GCA_013030945.1	1970	1970	type	True	84.9525	1528	2317	95	below_threshold
Streptomyces morookaense	strain=JCM 4793	GCA_014656115.1	1970	1970	type	True	84.9279	1581	2317	95	below_threshold
Streptomyces albireticuli	strain=NRRL B1670	GCA_021228125.1	1940	1940	type	True	84.8757	1570	2317	95	below_threshold
Streptomyces roseifaciens	strain=MBT76	GCA_001445655.1	1488406	1488406	type	True	84.8664	1569	2317	95	below_threshold
Streptomyces hiroshimensis	strain=JCM 4586	GCA_014650335.1	66424	66424	type	True	84.7528	1551	2317	95	below_threshold
Streptomyces huiliensis	strain=SCA2-4	GCA_020037025.1	2876027	2876027	type	True	83.785	1337	2317	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	81.4253	1187	2317	95	below_threshold
Streptomyces glomeratus	strain=DSM 41457	GCA_021462825.1	284452	284452	type	True	80.9175	1091	2317	95	below_threshold
Streptomyces ferrugineus	strain=CCTCC AA2014009	GCA_015160855.1	1413221	1413221	type	True	80.6957	1210	2317	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:23:16,081] [INFO] DFAST Taxonomy check result was written to GCF_014648775.1_ASM1464877v1_genomic.fna/tc_result.tsv
[2024-01-24 13:23:16,081] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:23:16,081] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:23:16,082] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdff510e5-3598-4e39-a0f0-ba8fdaac444b/dqc_reference/checkm_data
[2024-01-24 13:23:16,083] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:23:16,150] [INFO] Task started: CheckM
[2024-01-24 13:23:16,150] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014648775.1_ASM1464877v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014648775.1_ASM1464877v1_genomic.fna/checkm_input GCF_014648775.1_ASM1464877v1_genomic.fna/checkm_result
[2024-01-24 13:24:20,229] [INFO] Task succeeded: CheckM
[2024-01-24 13:24:20,230] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 9.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:24:20,257] [INFO] ===== Completeness check finished =====
[2024-01-24 13:24:20,258] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:24:20,258] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014648775.1_ASM1464877v1_genomic.fna/markers.fasta)
[2024-01-24 13:24:20,259] [INFO] Task started: Blastn
[2024-01-24 13:24:20,259] [INFO] Running command: blastn -query GCF_014648775.1_ASM1464877v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdff510e5-3598-4e39-a0f0-ba8fdaac444b/dqc_reference/reference_markers_gtdb.fasta -out GCF_014648775.1_ASM1464877v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:24:22,402] [INFO] Task succeeded: Blastn
[2024-01-24 13:24:22,407] [INFO] Selected 16 target genomes.
[2024-01-24 13:24:22,407] [INFO] Target genome list was writen to GCF_014648775.1_ASM1464877v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:24:22,601] [INFO] Task started: fastANI
[2024-01-24 13:24:22,601] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a347ab8-f44f-45ad-9215-5050e72a1d1e/GCF_014648775.1_ASM1464877v1_genomic.fna.gz --refList GCF_014648775.1_ASM1464877v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014648775.1_ASM1464877v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:24:53,245] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:53,272] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:24:53,272] [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_014648775.1	s__Streptomyces abikoensis	100.0	2316	2317	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.57	96.57	0.89	0.89	2	conclusive
GCA_000715685.1	s__Streptomyces lilacinus	87.2324	1613	2317	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650495.1	s__Streptomyces cinnamoneus	86.7822	1603	2317	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014655595.1	s__Streptomyces griseocarneus	86.778	1569	2317	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017349075.1	s__Streptomyces triculaminicus_A	86.5708	1599	2317	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.73	99.73	0.98	0.98	3	-
GCF_014203555.1	s__Streptomyces olivoverticillatus	86.3661	1407	2317	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002939475.1	s__Streptomyces cinnamoneus_A	86.2698	1553	2317	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014654785.1	s__Streptomyces mashuensis	85.1289	1519	2317	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013030945.1	s__Streptomyces morookaense	84.9678	1526	2317	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003011965.1	s__Streptomyces nondiastaticus	84.9538	1484	2317	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2548	N/A	N/A	N/A	N/A	1	-
GCF_001445655.1	s__Streptomyces roseifaciens	84.8323	1573	2317	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.65	95.65	0.88	0.88	2	-
GCF_014650335.1	s__Streptomyces hiroshimensis	84.7291	1555	2317	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003674045.1	s__Streptomyces griseocarneus_A	84.3261	1524	2317	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720325.1	s__Streptomyces sp000720325	80.9894	1293	2317	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018638295.1	s__Streptomyces sp018638295	80.9374	1071	2317	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015160855.1	s__Streptomyces ferrugineus	80.7183	1205	2317	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 13:24:53,273] [INFO] GTDB search result was written to GCF_014648775.1_ASM1464877v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:24:53,274] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:24:53,277] [INFO] DFAST_QC result json was written to GCF_014648775.1_ASM1464877v1_genomic.fna/dqc_result.json
[2024-01-24 13:24:53,277] [INFO] DFAST_QC completed!
[2024-01-24 13:24:53,278] [INFO] Total running time: 0h2m28s