[2024-01-24 12:53:37,281] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:37,283] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:37,283] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe48c0b7-7ff6-4752-ae17-e74084da90c1/dqc_reference
[2024-01-24 12:53:38,475] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:38,476] [INFO] Task started: Prodigal
[2024-01-24 12:53:38,476] [INFO] Running command: gunzip -c /var/lib/cwl/stg9155c389-cf22-4532-b1e4-9b0d2115247a/GCF_001642995.1_ASM164299v1_genomic.fna.gz | prodigal -d GCF_001642995.1_ASM164299v1_genomic.fna/cds.fna -a GCF_001642995.1_ASM164299v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:01,476] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:01,476] [INFO] Task started: HMMsearch
[2024-01-24 12:54:01,477] [INFO] Running command: hmmsearch --tblout GCF_001642995.1_ASM164299v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe48c0b7-7ff6-4752-ae17-e74084da90c1/dqc_reference/reference_markers.hmm GCF_001642995.1_ASM164299v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:01,830] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:01,832] [INFO] Found 6/6 markers.
[2024-01-24 12:54:01,894] [INFO] Query marker FASTA was written to GCF_001642995.1_ASM164299v1_genomic.fna/markers.fasta
[2024-01-24 12:54:01,895] [INFO] Task started: Blastn
[2024-01-24 12:54:01,895] [INFO] Running command: blastn -query GCF_001642995.1_ASM164299v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe48c0b7-7ff6-4752-ae17-e74084da90c1/dqc_reference/reference_markers.fasta -out GCF_001642995.1_ASM164299v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:03,165] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:03,169] [INFO] Selected 23 target genomes.
[2024-01-24 12:54:03,169] [INFO] Target genome list was writen to GCF_001642995.1_ASM164299v1_genomic.fna/target_genomes.txt
[2024-01-24 12:54:03,185] [INFO] Task started: fastANI
[2024-01-24 12:54:03,185] [INFO] Running command: fastANI --query /var/lib/cwl/stg9155c389-cf22-4532-b1e4-9b0d2115247a/GCF_001642995.1_ASM164299v1_genomic.fna.gz --refList GCF_001642995.1_ASM164299v1_genomic.fna/target_genomes.txt --output GCF_001642995.1_ASM164299v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:50,454] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:50,454] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe48c0b7-7ff6-4752-ae17-e74084da90c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:50,455] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe48c0b7-7ff6-4752-ae17-e74084da90c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:50,473] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:54:50,473] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:50,474] [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 jeddahensis	strain=G25	GCA_001642995.1	1716141	1716141	type	True	100.0	2708	2715	95	conclusive
Streptomyces himalayensis subsp. himalayensis	strain=PSKA28	GCA_013778455.1	2756131	2820085	type	True	90.9615	2055	2715	95	below_threshold
Streptomyces himalayensis subsp. aureolus	strain=PSKA54	GCA_013912435.1	2758039	2820085	type	True	90.9304	2037	2715	95	below_threshold
Streptomyces albiflavescens	strain=CGMCC 4.7111	GCA_014645835.1	1623582	1623582	type	True	83.5866	1677	2715	95	below_threshold
Streptomyces avermitilis	strain=DSM 46492	GCA_001514135.1	33903	33903	type	True	83.5513	1565	2715	95	below_threshold
Streptomyces phyllanthi	strain=TISTR 2346	GCA_009377205.1	1803180	1803180	type	True	83.5356	1452	2715	95	below_threshold
Streptomyces avermitilis	strain=NBRC 14893	GCA_005405965.1	33903	33903	type	True	83.5248	1603	2715	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	83.4727	1631	2715	95	below_threshold
Streptomyces minutiscleroticus	strain=JCM 4790	GCA_014650875.1	68238	68238	type	True	83.4421	1471	2715	95	below_threshold
Streptomyces umbrinus	strain=JCM 4521	GCA_014650195.1	67370	67370	type	True	83.3541	1681	2715	95	below_threshold
Streptomyces cahuitamycinicus	strain=13K301	GCA_002891435.1	2070367	2070367	type	True	83.3482	1365	2715	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	83.2808	1539	2715	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	83.0608	1659	2715	95	below_threshold
Streptomyces kebangsaanensis	strain=SUK12	GCA_001906585.1	864058	864058	type	True	83.0218	1369	2715	95	below_threshold
Streptomyces glomeratus	strain=DSM 41457	GCA_021462825.1	284452	284452	type	True	83.0018	1374	2715	95	below_threshold
Streptomyces durmitorensis	strain=MS405	GCA_023498005.1	319947	319947	type	True	82.9148	1523	2715	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	82.8295	1471	2715	95	below_threshold
Streptomyces flavofungini	strain=JCM 4753	GCA_016411765.1	68200	68200	type	True	82.7118	1455	2715	95	below_threshold
Streptomyces flavofungini	strain=JCM 4753	GCA_014650815.1	68200	68200	type	True	82.5947	1444	2715	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	82.5475	1457	2715	95	below_threshold
Streptomyces monashensis	strain=MUSC 1	GCA_001866665.1	1678012	1678012	type	True	82.444	1526	2715	95	below_threshold
Streptomyces litmocidini	strain=JCM 4394	GCA_014649755.1	67318	67318	type	True	81.8034	1277	2715	95	below_threshold
Streptomyces tanashiensis	strain=JCM 4086	GCA_014648895.1	67367	67367	type	True	81.5732	1320	2715	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:50,475] [INFO] DFAST Taxonomy check result was written to GCF_001642995.1_ASM164299v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:50,476] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:50,476] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:50,476] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe48c0b7-7ff6-4752-ae17-e74084da90c1/dqc_reference/checkm_data
[2024-01-24 12:54:50,477] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:50,554] [INFO] Task started: CheckM
[2024-01-24 12:54:50,554] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001642995.1_ASM164299v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001642995.1_ASM164299v1_genomic.fna/checkm_input GCF_001642995.1_ASM164299v1_genomic.fna/checkm_result
[2024-01-24 12:56:07,412] [INFO] Task succeeded: CheckM
[2024-01-24 12:56:07,414] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:56:07,441] [INFO] ===== Completeness check finished =====
[2024-01-24 12:56:07,441] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:56:07,442] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001642995.1_ASM164299v1_genomic.fna/markers.fasta)
[2024-01-24 12:56:07,442] [INFO] Task started: Blastn
[2024-01-24 12:56:07,442] [INFO] Running command: blastn -query GCF_001642995.1_ASM164299v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe48c0b7-7ff6-4752-ae17-e74084da90c1/dqc_reference/reference_markers_gtdb.fasta -out GCF_001642995.1_ASM164299v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:56:09,436] [INFO] Task succeeded: Blastn
[2024-01-24 12:56:09,441] [INFO] Selected 25 target genomes.
[2024-01-24 12:56:09,441] [INFO] Target genome list was writen to GCF_001642995.1_ASM164299v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:56:09,479] [INFO] Task started: fastANI
[2024-01-24 12:56:09,479] [INFO] Running command: fastANI --query /var/lib/cwl/stg9155c389-cf22-4532-b1e4-9b0d2115247a/GCF_001642995.1_ASM164299v1_genomic.fna.gz --refList GCF_001642995.1_ASM164299v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001642995.1_ASM164299v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:57:00,144] [INFO] Task succeeded: fastANI
[2024-01-24 12:57:00,165] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:57:00,165] [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_001642995.1	s__Streptomyces jeddahensis	100.0	2708	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013778455.1	s__Streptomyces himalayensis	90.9743	2054	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.53	97.53	0.86	0.86	2	-
GCF_008905045.1	s__Streptomyces albicerus	83.6824	1787	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014645835.1	s__Streptomyces albiflavescens	83.5728	1683	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539505.1	s__Streptomyces spinoverrucosus	83.5573	1591	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.41	95.17	0.85	0.79	5	-
GCF_009377205.1	s__Streptomyces phyllanthi	83.4839	1462	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650875.1	s__Streptomyces minutiscleroticus	83.4644	1467	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.56	98.56	0.90	0.90	2	-
GCF_007050945.1	s__Streptomyces sp007050945	83.4005	1715	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016598615.1	s__Streptomyces sp016598615	83.3529	1692	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014596915.1	s__Streptomyces sp014596915	83.2708	1557	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009852415.1	s__Streptomyces sp009852415	83.231	1489	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001417775.1	s__Streptomyces sp001417775	83.1747	1452	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003248315.1	s__Streptomyces sp003248315	83.1305	1459	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002920535.1	s__Streptomyces sp002920535	83.0438	1497	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015160875.1	s__Streptomyces chromofuscus	83.0181	1425	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	0.98	0.98	2	-
GCF_001906585.1	s__Streptomyces kebangsaanensis	83.0078	1372	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002154505.1	s__Streptomyces carpinensis	83.0072	1406	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009769735.1	s__Streptomyces sp009769735	82.9353	1527	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646335.1	s__Streptomyces lasiicapitis	82.6266	1465	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.86	98.86	0.95	0.95	2	-
GCF_014650815.1	s__Streptomyces flavofungini	82.6235	1440	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	0.99	0.99	2	-
GCF_016741775.1	s__Streptomyces actinomycinicus	82.6001	1398	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720185.1	s__Streptomyces sp000720185	82.4415	1416	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001866665.1	s__Streptomyces monashensis	82.4286	1527	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.09	95.09	0.78	0.78	2	-
GCF_001905665.1	s__Streptomyces sp001905665	81.655	1268	2715	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003391135.1	s__Streptomyces olivoreticuli	81.1054	1114	2715	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 12:57:00,167] [INFO] GTDB search result was written to GCF_001642995.1_ASM164299v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:57:00,168] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:57:00,172] [INFO] DFAST_QC result json was written to GCF_001642995.1_ASM164299v1_genomic.fna/dqc_result.json
[2024-01-24 12:57:00,173] [INFO] DFAST_QC completed!
[2024-01-24 12:57:00,173] [INFO] Total running time: 0h3m23s