[2024-01-24 13:50:26,549] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:50:26,551] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:50:26,551] [INFO] DQC Reference Directory: /var/lib/cwl/stg58522594-ba4f-4dd0-8653-0edd3e8d2cd7/dqc_reference
[2024-01-24 13:50:27,759] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:50:27,760] [INFO] Task started: Prodigal
[2024-01-24 13:50:27,760] [INFO] Running command: gunzip -c /var/lib/cwl/stg8b8581db-cd8f-49d6-8091-f72511f68e25/GCF_018883605.1_ASM1888360v1_genomic.fna.gz | prodigal -d GCF_018883605.1_ASM1888360v1_genomic.fna/cds.fna -a GCF_018883605.1_ASM1888360v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:57,384] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:57,384] [INFO] Task started: HMMsearch
[2024-01-24 13:50:57,385] [INFO] Running command: hmmsearch --tblout GCF_018883605.1_ASM1888360v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg58522594-ba4f-4dd0-8653-0edd3e8d2cd7/dqc_reference/reference_markers.hmm GCF_018883605.1_ASM1888360v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:57,765] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:57,766] [INFO] Found 6/6 markers.
[2024-01-24 13:50:57,843] [INFO] Query marker FASTA was written to GCF_018883605.1_ASM1888360v1_genomic.fna/markers.fasta
[2024-01-24 13:50:57,844] [INFO] Task started: Blastn
[2024-01-24 13:50:57,844] [INFO] Running command: blastn -query GCF_018883605.1_ASM1888360v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg58522594-ba4f-4dd0-8653-0edd3e8d2cd7/dqc_reference/reference_markers.fasta -out GCF_018883605.1_ASM1888360v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:59,084] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:59,088] [INFO] Selected 15 target genomes.
[2024-01-24 13:50:59,088] [INFO] Target genome list was writen to GCF_018883605.1_ASM1888360v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:59,122] [INFO] Task started: fastANI
[2024-01-24 13:50:59,122] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b8581db-cd8f-49d6-8091-f72511f68e25/GCF_018883605.1_ASM1888360v1_genomic.fna.gz --refList GCF_018883605.1_ASM1888360v1_genomic.fna/target_genomes.txt --output GCF_018883605.1_ASM1888360v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:51:37,227] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:37,228] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg58522594-ba4f-4dd0-8653-0edd3e8d2cd7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:51:37,228] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg58522594-ba4f-4dd0-8653-0edd3e8d2cd7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:51:37,240] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:51:37,240] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:51:37,240] [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 yatensis	strain=DSM 41771	GCA_018069625.1	155177	155177	type	True	94.5258	2402	3039	95	below_threshold
Streptomyces antimycoticus	strain=NBRC 12839	GCA_005405925.1	68175	68175	type	True	94.4088	2420	3039	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_003675955.1	1226757	1226757	type	True	91.642	2357	3039	95	below_threshold
Streptomyces iranensis	strain=DSM 41954	GCA_017874715.1	576784	576784	type	True	91.6124	2342	3039	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_024298965.1	1226757	1226757	type	True	91.5781	2351	3039	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_000418455.1	1226757	1226757	type	True	91.5663	2376	3039	95	below_threshold
Streptomyces sabulosicollis	strain=PRKS01-29	GCA_016103465.1	2715963	2715963	type	True	91.4418	1893	3039	95	below_threshold
Streptomyces javensis	strain=DSM 41764	GCA_016103505.1	114698	114698	type	True	91.3101	1862	3039	95	below_threshold
Streptomyces hygroscopicus subsp. hygroscopicus	strain=NBRC 13472	GCA_001553455.1	68042	1912	type	True	90.0836	1878	3039	95	below_threshold
Streptomyces palmae	strain=JCM 31289	GCA_004684805.1	1701085	1701085	type	True	81.9812	1123	3039	95	below_threshold
Streptomyces pactum	strain=ATCC 27456	GCA_016031615.1	68249	68249	type	True	81.3164	1285	3039	95	below_threshold
Streptomyces albireticuli	strain=NRRL B1670	GCA_021228125.1	1940	1940	type	True	80.9286	1232	3039	95	below_threshold
Streptomyces rimosus subsp. rimosus	strain=R7	GCA_022760195.1	132474	1927	type	True	80.7807	1359	3039	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	80.6889	1165	3039	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	80.2406	1142	3039	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:51:37,245] [INFO] DFAST Taxonomy check result was written to GCF_018883605.1_ASM1888360v1_genomic.fna/tc_result.tsv
[2024-01-24 13:51:37,246] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:51:37,246] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:51:37,246] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg58522594-ba4f-4dd0-8653-0edd3e8d2cd7/dqc_reference/checkm_data
[2024-01-24 13:51:37,247] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:51:37,348] [INFO] Task started: CheckM
[2024-01-24 13:51:37,348] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018883605.1_ASM1888360v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018883605.1_ASM1888360v1_genomic.fna/checkm_input GCF_018883605.1_ASM1888360v1_genomic.fna/checkm_result
[2024-01-24 13:53:11,160] [INFO] Task succeeded: CheckM
[2024-01-24 13:53:11,161] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:53:11,191] [INFO] ===== Completeness check finished =====
[2024-01-24 13:53:11,191] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:53:11,192] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018883605.1_ASM1888360v1_genomic.fna/markers.fasta)
[2024-01-24 13:53:11,192] [INFO] Task started: Blastn
[2024-01-24 13:53:11,192] [INFO] Running command: blastn -query GCF_018883605.1_ASM1888360v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg58522594-ba4f-4dd0-8653-0edd3e8d2cd7/dqc_reference/reference_markers_gtdb.fasta -out GCF_018883605.1_ASM1888360v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:53:13,185] [INFO] Task succeeded: Blastn
[2024-01-24 13:53:13,190] [INFO] Selected 9 target genomes.
[2024-01-24 13:53:13,190] [INFO] Target genome list was writen to GCF_018883605.1_ASM1888360v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:53:13,277] [INFO] Task started: fastANI
[2024-01-24 13:53:13,277] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b8581db-cd8f-49d6-8091-f72511f68e25/GCF_018883605.1_ASM1888360v1_genomic.fna.gz --refList GCF_018883605.1_ASM1888360v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018883605.1_ASM1888360v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:53:43,000] [INFO] Task succeeded: fastANI
[2024-01-24 13:53:43,009] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:53:43,009] [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_000147815.2	s__Streptomyces violaceusniger_A	94.7109	2387	3039	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3301	95.69	95.54	0.80	0.80	4	-
GCF_018069625.1	s__Streptomyces yatensis	94.548	2399	3039	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.0185	N/A	N/A	N/A	N/A	1	-
GCF_005405925.1	s__Streptomyces antimycoticus	94.4387	2416	3039	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.0185	97.28	96.80	0.85	0.81	7	-
GCF_016741935.1	s__Streptomyces sp016741935	91.9791	2492	3039	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	91.6138	2343	3039	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.17	95.36	0.90	0.81	10	-
GCF_017874715.1	s__Streptomyces iranensis	91.6137	2342	3039	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.67	99.98	99.98	1.00	1.00	2	-
GCF_015689475.1	s__Streptomyces solisilvae	91.4228	2273	3039	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.71	97.94	0.94	0.86	10	-
GCA_005405945.1	s__Streptomyces violaceusniger	91.3681	2266	3039	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.67	97.67	0.85	0.85	2	-
GCF_001553455.1	s__Streptomyces hygroscopicus	90.0901	1876	3039	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.24	98.00	0.92	0.90	7	-
--------------------------------------------------------------------------------
[2024-01-24 13:53:43,011] [INFO] GTDB search result was written to GCF_018883605.1_ASM1888360v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:53:43,012] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:53:43,017] [INFO] DFAST_QC result json was written to GCF_018883605.1_ASM1888360v1_genomic.fna/dqc_result.json
[2024-01-24 13:53:43,017] [INFO] DFAST_QC completed!
[2024-01-24 13:53:43,017] [INFO] Total running time: 0h3m16s