[2024-01-25 17:47:35,619] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:47:35,620] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:47:35,620] [INFO] DQC Reference Directory: /var/lib/cwl/stg6a00ed98-28a2-42b5-a0de-0f7893953182/dqc_reference
[2024-01-25 17:47:36,771] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:47:36,772] [INFO] Task started: Prodigal
[2024-01-25 17:47:36,772] [INFO] Running command: gunzip -c /var/lib/cwl/stg9b265201-a8f3-40e4-9ccd-cf65ce8296f0/GCF_014649795.1_ASM1464979v1_genomic.fna.gz | prodigal -d GCF_014649795.1_ASM1464979v1_genomic.fna/cds.fna -a GCF_014649795.1_ASM1464979v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:48:00,997] [INFO] Task succeeded: Prodigal
[2024-01-25 17:48:00,998] [INFO] Task started: HMMsearch
[2024-01-25 17:48:00,998] [INFO] Running command: hmmsearch --tblout GCF_014649795.1_ASM1464979v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6a00ed98-28a2-42b5-a0de-0f7893953182/dqc_reference/reference_markers.hmm GCF_014649795.1_ASM1464979v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:48:01,325] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:48:01,326] [INFO] Found 6/6 markers.
[2024-01-25 17:48:01,394] [INFO] Query marker FASTA was written to GCF_014649795.1_ASM1464979v1_genomic.fna/markers.fasta
[2024-01-25 17:48:01,394] [INFO] Task started: Blastn
[2024-01-25 17:48:01,394] [INFO] Running command: blastn -query GCF_014649795.1_ASM1464979v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a00ed98-28a2-42b5-a0de-0f7893953182/dqc_reference/reference_markers.fasta -out GCF_014649795.1_ASM1464979v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:48:02,641] [INFO] Task succeeded: Blastn
[2024-01-25 17:48:02,644] [INFO] Selected 23 target genomes.
[2024-01-25 17:48:02,644] [INFO] Target genome list was writen to GCF_014649795.1_ASM1464979v1_genomic.fna/target_genomes.txt
[2024-01-25 17:48:02,656] [INFO] Task started: fastANI
[2024-01-25 17:48:02,656] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b265201-a8f3-40e4-9ccd-cf65ce8296f0/GCF_014649795.1_ASM1464979v1_genomic.fna.gz --refList GCF_014649795.1_ASM1464979v1_genomic.fna/target_genomes.txt --output GCF_014649795.1_ASM1464979v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:48:51,637] [INFO] Task succeeded: fastANI
[2024-01-25 17:48:51,638] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6a00ed98-28a2-42b5-a0de-0f7893953182/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:48:51,638] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6a00ed98-28a2-42b5-a0de-0f7893953182/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:48:51,651] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:48:51,652] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:48:51,652] [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 melanogenes	strain=JCM 4398	GCA_014649795.1	67326	67326	type	True	100.0	3140	3144	95	conclusive
Streptomyces violascens	strain=NBRC 12920	GCA_020521295.1	67381	67381	type	True	85.2169	1736	3144	95	below_threshold
Streptomyces violascens	strain=JCM 4424	GCA_014649955.1	67381	67381	type	True	85.2033	1728	3144	95	below_threshold
Streptomyces xanthochromogenes	strain=JCM 4612	GCA_014650455.1	67384	67384	type	True	84.7709	1705	3144	95	below_threshold
Streptomyces lunaelactis	strain=MM109	GCA_003054555.1	1535768	1535768	type	True	83.3459	1474	3144	95	below_threshold
Streptomyces purpureus	strain=JCM 3172	GCA_014648195.1	1951	1951	type	True	83.334	1485	3144	95	below_threshold
Streptomyces lateritius	strain=JCM 4389	GCA_014649715.1	67313	67313	type	True	83.021	1497	3144	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	83.0084	1503	3144	95	below_threshold
Streptomyces nymphaeiformis	strain=SFB5A	GCA_014203895.1	2663842	2663842	type	True	82.9502	1575	3144	95	below_threshold
Streptomyces litmocidini	strain=JCM 4394	GCA_014649755.1	67318	67318	type	True	82.9336	1502	3144	95	below_threshold
Streptomyces lavendofoliae	strain=JCM 4391	GCA_014649735.1	67314	67314	type	True	82.8847	1419	3144	95	below_threshold
Streptomyces wuyuanensis	strain=CGMCC 4.7042	GCA_900103455.1	1196353	1196353	type	True	82.446	1453	3144	95	below_threshold
Streptomyces alfalfae	strain=XY25	GCA_004212445.1	1642299	1642299	type	True	82.4352	1427	3144	95	below_threshold
Streptomyces alfalfae	strain=XY25	GCA_004127445.1	1642299	1642299	type	True	82.4016	1488	3144	95	below_threshold
Streptomyces zhihengii	strain=YIM T102	GCA_016919245.1	1818004	1818004	type	True	82.3363	1521	3144	95	below_threshold
Streptomyces genisteinicus	strain=CRPJ-33	GCA_014489615.1	2768068	2768068	type	True	82.2778	1459	3144	95	below_threshold
Streptomyces vinaceus	strain=JCM 4849	GCA_014656155.1	1960	1960	type	True	82.2723	1477	3144	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	82.2209	1079	3144	95	below_threshold
Streptomyces vinaceus	strain=ATCC 27476	GCA_008704935.1	1960	1960	type	True	82.2091	1488	3144	95	below_threshold
Streptomyces yangpuensis	strain=fd2-tb	GCA_001005295.1	1648182	1648182	type	True	82.1048	1387	3144	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	81.8482	1478	3144	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	81.8397	1269	3144	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	81.7771	1344	3144	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:48:51,653] [INFO] DFAST Taxonomy check result was written to GCF_014649795.1_ASM1464979v1_genomic.fna/tc_result.tsv
[2024-01-25 17:48:51,654] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:48:51,654] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:48:51,654] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6a00ed98-28a2-42b5-a0de-0f7893953182/dqc_reference/checkm_data
[2024-01-25 17:48:51,655] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:48:51,742] [INFO] Task started: CheckM
[2024-01-25 17:48:51,742] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014649795.1_ASM1464979v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014649795.1_ASM1464979v1_genomic.fna/checkm_input GCF_014649795.1_ASM1464979v1_genomic.fna/checkm_result
[2024-01-25 17:50:26,349] [INFO] Task succeeded: CheckM
[2024-01-25 17:50:26,350] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:50:26,399] [INFO] ===== Completeness check finished =====
[2024-01-25 17:50:26,399] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:50:26,400] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014649795.1_ASM1464979v1_genomic.fna/markers.fasta)
[2024-01-25 17:50:26,400] [INFO] Task started: Blastn
[2024-01-25 17:50:26,400] [INFO] Running command: blastn -query GCF_014649795.1_ASM1464979v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a00ed98-28a2-42b5-a0de-0f7893953182/dqc_reference/reference_markers_gtdb.fasta -out GCF_014649795.1_ASM1464979v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:50:28,584] [INFO] Task succeeded: Blastn
[2024-01-25 17:50:28,588] [INFO] Selected 12 target genomes.
[2024-01-25 17:50:28,588] [INFO] Target genome list was writen to GCF_014649795.1_ASM1464979v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:50:28,606] [INFO] Task started: fastANI
[2024-01-25 17:50:28,606] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b265201-a8f3-40e4-9ccd-cf65ce8296f0/GCF_014649795.1_ASM1464979v1_genomic.fna.gz --refList GCF_014649795.1_ASM1464979v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014649795.1_ASM1464979v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:50:56,936] [INFO] Task succeeded: fastANI
[2024-01-25 17:50:56,944] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:50:56,944] [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_014649795.1	s__Streptomyces melanogenes	100.0	3140	3144	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.19	95.19	0.83	0.83	2	conclusive
GCF_001653515.1	s__Streptomyces sp001653515	92.4967	1973	3144	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014596475.1	s__Streptomyces sp014596475	89.3465	2069	3144	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001279695.1	s__Streptomyces sp001279695	85.2904	1758	3144	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003324565.1	s__Streptomyces sp003324565	85.2244	1736	3144	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649955.1	s__Streptomyces violascens	85.1657	1735	3144	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003627815.1	s__Streptomyces hundungensis	84.71	1700	3144	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054555.1	s__Streptomyces lunaelactis	83.3355	1476	3144	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.21	97.91	0.90	0.85	18	-
GCF_014648195.1	s__Streptomyces purpureus	83.3119	1489	3144	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.54	99.54	0.95	0.95	2	-
GCF_004353505.1	s__Streptomyces sp004353505	83.2486	1416	3144	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.95	99.86	0.97	0.92	4	-
GCF_018614205.1	s__Streptomyces sp018614205	83.0442	1436	3144	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720115.1	s__Streptomyces sp000720115	82.1387	1441	3144	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:50:56,946] [INFO] GTDB search result was written to GCF_014649795.1_ASM1464979v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:50:56,947] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:50:56,950] [INFO] DFAST_QC result json was written to GCF_014649795.1_ASM1464979v1_genomic.fna/dqc_result.json
[2024-01-25 17:50:56,950] [INFO] DFAST_QC completed!
[2024-01-25 17:50:56,950] [INFO] Total running time: 0h3m21s