[2024-01-24 13:49:31,980] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:31,982] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:31,982] [INFO] DQC Reference Directory: /var/lib/cwl/stg0c54e179-0211-4033-bdb9-8f4c97728f19/dqc_reference
[2024-01-24 13:49:33,342] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:33,347] [INFO] Task started: Prodigal
[2024-01-24 13:49:33,348] [INFO] Running command: gunzip -c /var/lib/cwl/stg537aa863-22d7-459f-8857-e4f3b3ae56d2/GCF_014648195.1_ASM1464819v1_genomic.fna.gz | prodigal -d GCF_014648195.1_ASM1464819v1_genomic.fna/cds.fna -a GCF_014648195.1_ASM1464819v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:53,733] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:53,734] [INFO] Task started: HMMsearch
[2024-01-24 13:49:53,734] [INFO] Running command: hmmsearch --tblout GCF_014648195.1_ASM1464819v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0c54e179-0211-4033-bdb9-8f4c97728f19/dqc_reference/reference_markers.hmm GCF_014648195.1_ASM1464819v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:54,210] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:54,211] [INFO] Found 6/6 markers.
[2024-01-24 13:49:54,273] [INFO] Query marker FASTA was written to GCF_014648195.1_ASM1464819v1_genomic.fna/markers.fasta
[2024-01-24 13:49:54,274] [INFO] Task started: Blastn
[2024-01-24 13:49:54,274] [INFO] Running command: blastn -query GCF_014648195.1_ASM1464819v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c54e179-0211-4033-bdb9-8f4c97728f19/dqc_reference/reference_markers.fasta -out GCF_014648195.1_ASM1464819v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:55,720] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:55,723] [INFO] Selected 20 target genomes.
[2024-01-24 13:49:55,724] [INFO] Target genome list was writen to GCF_014648195.1_ASM1464819v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:55,728] [INFO] Task started: fastANI
[2024-01-24 13:49:55,729] [INFO] Running command: fastANI --query /var/lib/cwl/stg537aa863-22d7-459f-8857-e4f3b3ae56d2/GCF_014648195.1_ASM1464819v1_genomic.fna.gz --refList GCF_014648195.1_ASM1464819v1_genomic.fna/target_genomes.txt --output GCF_014648195.1_ASM1464819v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:33,765] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:33,765] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0c54e179-0211-4033-bdb9-8f4c97728f19/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:33,766] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0c54e179-0211-4033-bdb9-8f4c97728f19/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:33,783] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:33,783] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:33,784] [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 purpureus	strain=JCM 3172	GCA_014648195.1	1951	1951	type	True	100.0	2471	2475	95	conclusive
Streptomyces lateritius	strain=JCM 4389	GCA_014649715.1	67313	67313	type	True	85.2582	1615	2475	95	below_threshold
Streptomyces venezuelae	strain=ATCC 10712	GCA_021432215.1	54571	54571	type	True	84.8841	1250	2475	95	below_threshold
Streptomyces cinereoruber	strain=JCM 4205	GCA_014649095.1	67260	67260	type	True	84.6191	1459	2475	95	below_threshold
Streptomyces tanashiensis	strain=JCM 4086	GCA_014648895.1	67367	67367	type	True	84.5901	1610	2475	95	below_threshold
Streptomyces litmocidini	strain=JCM 4394	GCA_014649755.1	67318	67318	type	True	84.5656	1537	2475	95	below_threshold
Streptomyces cinereoruber	strain=JCM4205	GCA_019880525.1	67260	67260	type	True	84.5602	1488	2475	95	below_threshold
Streptomyces cinereoruber	strain=NRRL ISP-5012	GCA_014197485.1	67260	67260	type	True	84.5469	1486	2475	95	below_threshold
Streptomyces cinereoruber	strain=ATCC 19740	GCA_009299385.1	67260	67260	type	True	84.5413	1517	2475	95	below_threshold
Streptomyces vietnamensis	strain=GIM4.0001	GCA_000830005.1	362257	362257	type	True	84.437	1626	2475	95	below_threshold
Streptomyces lavendofoliae	strain=JCM 4391	GCA_014649735.1	67314	67314	type	True	84.3782	1453	2475	95	below_threshold
Streptomyces wedmorensis	strain=NRRL 3426	GCA_000716445.1	43759	43759	type	True	84.3699	1576	2475	95	below_threshold
Streptomyces omiyaensis	strain=JCM 4806	GCA_014650895.1	68247	68247	type	True	84.0504	1549	2475	95	below_threshold
Streptomyces termitum	strain=JCM 4518	GCA_014650175.1	67368	67368	type	True	84.0296	1469	2475	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	83.9683	1486	2475	95	below_threshold
Streptomyces melanogenes	strain=JCM 4398	GCA_014649795.1	67326	67326	type	True	83.3044	1508	2475	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	83.258	1369	2475	95	below_threshold
Streptomyces somaliensis	strain=DSM 40738	GCA_024349285.1	78355	78355	type	True	83.1164	1100	2475	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	83.0593	1112	2475	95	below_threshold
Streptomyces atratus	strain=JCM 3386	GCA_014648655.1	1893	1893	suspected-type	True	82.6074	1406	2475	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:33,785] [INFO] DFAST Taxonomy check result was written to GCF_014648195.1_ASM1464819v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:33,785] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:33,786] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:33,786] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0c54e179-0211-4033-bdb9-8f4c97728f19/dqc_reference/checkm_data
[2024-01-24 13:50:33,787] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:33,856] [INFO] Task started: CheckM
[2024-01-24 13:50:33,856] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014648195.1_ASM1464819v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014648195.1_ASM1464819v1_genomic.fna/checkm_input GCF_014648195.1_ASM1464819v1_genomic.fna/checkm_result
[2024-01-24 13:52:04,982] [INFO] Task succeeded: CheckM
[2024-01-24 13:52:04,984] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:52:05,007] [INFO] ===== Completeness check finished =====
[2024-01-24 13:52:05,007] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:52:05,008] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014648195.1_ASM1464819v1_genomic.fna/markers.fasta)
[2024-01-24 13:52:05,008] [INFO] Task started: Blastn
[2024-01-24 13:52:05,008] [INFO] Running command: blastn -query GCF_014648195.1_ASM1464819v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c54e179-0211-4033-bdb9-8f4c97728f19/dqc_reference/reference_markers_gtdb.fasta -out GCF_014648195.1_ASM1464819v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:52:07,148] [INFO] Task succeeded: Blastn
[2024-01-24 13:52:07,152] [INFO] Selected 16 target genomes.
[2024-01-24 13:52:07,153] [INFO] Target genome list was writen to GCF_014648195.1_ASM1464819v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:52:07,189] [INFO] Task started: fastANI
[2024-01-24 13:52:07,189] [INFO] Running command: fastANI --query /var/lib/cwl/stg537aa863-22d7-459f-8857-e4f3b3ae56d2/GCF_014648195.1_ASM1464819v1_genomic.fna.gz --refList GCF_014648195.1_ASM1464819v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014648195.1_ASM1464819v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:52:37,041] [INFO] Task succeeded: fastANI
[2024-01-24 13:52:37,060] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:52:37,060] [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_014648195.1	s__Streptomyces purpureus	100.0	2471	2475	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.54	99.54	0.95	0.95	2	conclusive
GCF_018614205.1	s__Streptomyces sp018614205	85.4617	1523	2475	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005517195.1	s__Streptomyces exfoliatus_B	85.3587	1643	2475	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008042125.1	s__Streptomyces sp008042125	84.9893	1555	2475	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105415.1	s__Streptomyces sp900105415	84.659	1603	2475	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.65	95.65	0.85	0.85	2	-
GCF_001280125.1	s__Streptomyces sp001280125	84.5732	1459	2475	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.57	95.16	0.89	0.81	3	-
GCF_014649755.1	s__Streptomyces litmocidini	84.5532	1538	2475	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.07	95.07	0.85	0.85	2	-
GCF_001008345.1	s__Streptomyces showdoensis	84.5487	1502	2475	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009739905.1	s__Streptomyces ficellus	84.5165	1520	2475	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000716445.1	s__Streptomyces wedmorensis	84.4005	1569	2475	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.81	97.63	0.94	0.88	3	-
GCF_001646665.1	s__Streptomyces albulus_A	84.383	1486	2475	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649735.1	s__Streptomyces lavendofoliae	84.379	1453	2475	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000716335.1	s__Streptomyces sp000716335	84.1948	1533	2475	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008271805.1	s__Streptomyces sp008271805	83.7515	1387	2475	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001653515.1	s__Streptomyces sp001653515	83.4167	1267	2475	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649795.1	s__Streptomyces melanogenes	83.3198	1506	2475	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.19	95.19	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:52:37,062] [INFO] GTDB search result was written to GCF_014648195.1_ASM1464819v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:52:37,063] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:52:37,070] [INFO] DFAST_QC result json was written to GCF_014648195.1_ASM1464819v1_genomic.fna/dqc_result.json
[2024-01-24 13:52:37,070] [INFO] DFAST_QC completed!
[2024-01-24 13:52:37,070] [INFO] Total running time: 0h3m5s