[2023-06-30 12:04:40,687] [INFO] DFAST_QC pipeline started.
[2023-06-30 12:04:40,690] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 12:04:40,690] [INFO] DQC Reference Directory: /var/lib/cwl/stgd058ef51-4939-49f1-b8e3-c4c88730c366/dqc_reference
[2023-06-30 12:04:41,959] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 12:04:41,960] [INFO] Task started: Prodigal
[2023-06-30 12:04:41,960] [INFO] Running command: gunzip -c /var/lib/cwl/stg5e8714b0-82a2-4c6a-983a-8fedcd83e772/GCA_025363815.1_ASM2536381v1_genomic.fna.gz | prodigal -d GCA_025363815.1_ASM2536381v1_genomic.fna/cds.fna -a GCA_025363815.1_ASM2536381v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 12:04:49,758] [INFO] Task succeeded: Prodigal
[2023-06-30 12:04:49,758] [INFO] Task started: HMMsearch
[2023-06-30 12:04:49,758] [INFO] Running command: hmmsearch --tblout GCA_025363815.1_ASM2536381v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd058ef51-4939-49f1-b8e3-c4c88730c366/dqc_reference/reference_markers.hmm GCA_025363815.1_ASM2536381v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 12:04:50,012] [INFO] Task succeeded: HMMsearch
[2023-06-30 12:04:50,014] [INFO] Found 6/6 markers.
[2023-06-30 12:04:50,046] [INFO] Query marker FASTA was written to GCA_025363815.1_ASM2536381v1_genomic.fna/markers.fasta
[2023-06-30 12:04:50,047] [INFO] Task started: Blastn
[2023-06-30 12:04:50,047] [INFO] Running command: blastn -query GCA_025363815.1_ASM2536381v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd058ef51-4939-49f1-b8e3-c4c88730c366/dqc_reference/reference_markers.fasta -out GCA_025363815.1_ASM2536381v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 12:04:50,794] [INFO] Task succeeded: Blastn
[2023-06-30 12:04:50,799] [INFO] Selected 20 target genomes.
[2023-06-30 12:04:50,799] [INFO] Target genome list was writen to GCA_025363815.1_ASM2536381v1_genomic.fna/target_genomes.txt
[2023-06-30 12:04:50,805] [INFO] Task started: fastANI
[2023-06-30 12:04:50,806] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e8714b0-82a2-4c6a-983a-8fedcd83e772/GCA_025363815.1_ASM2536381v1_genomic.fna.gz --refList GCA_025363815.1_ASM2536381v1_genomic.fna/target_genomes.txt --output GCA_025363815.1_ASM2536381v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 12:05:06,393] [INFO] Task succeeded: fastANI
[2023-06-30 12:05:06,394] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd058ef51-4939-49f1-b8e3-c4c88730c366/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 12:05:06,394] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd058ef51-4939-49f1-b8e3-c4c88730c366/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 12:05:06,411] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 12:05:06,411] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 12:05:06,411] [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
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	76.3089	102	863	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	76.2575	114	863	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	76.1589	129	863	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	75.751	95	863	95	below_threshold
Ilumatobacter nonamiensis	strain=YM16-303	GCA_000350145.1	467093	467093	type	True	75.6531	70	863	95	below_threshold
Egicoccus halophilus	strain=CGMCC 1.14988	GCA_014640475.1	1670830	1670830	type	True	75.6445	68	863	95	below_threshold
Egicoccus halophilus	strain=EGI 80432	GCA_004300825.1	1670830	1670830	type	True	75.6278	69	863	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	75.5548	106	863	95	below_threshold
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	75.3447	84	863	95	below_threshold
Actinoplanes tereljensis	strain=NBRC 105297	GCA_016862435.1	571912	571912	type	True	75.1652	111	863	95	below_threshold
Asanoa ishikariensis	strain=NBRC 14551	GCA_016862535.1	137265	137265	type	True	75.1625	95	863	95	below_threshold
Asanoa ishikariensis	strain=DSM 44718	GCA_900107455.1	137265	137265	type	True	75.1553	93	863	95	below_threshold
Virgisporangium aliadipatigenens	strain=NBRC 105644	GCA_016863615.1	741659	741659	type	True	75.1294	106	863	95	below_threshold
Actinoplanes toevensis	strain=NBRC 105298	GCA_018332695.1	571911	571911	type	True	75.1166	114	863	95	below_threshold
Amycolatopsis acidicola	strain=K81G1	GCA_007713735.2	2596893	2596893	type	True	74.8558	97	863	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 12:05:06,413] [INFO] DFAST Taxonomy check result was written to GCA_025363815.1_ASM2536381v1_genomic.fna/tc_result.tsv
[2023-06-30 12:05:06,414] [INFO] ===== Taxonomy check completed =====
[2023-06-30 12:05:06,414] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 12:05:06,415] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd058ef51-4939-49f1-b8e3-c4c88730c366/dqc_reference/checkm_data
[2023-06-30 12:05:06,416] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 12:05:06,452] [INFO] Task started: CheckM
[2023-06-30 12:05:06,452] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_025363815.1_ASM2536381v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_025363815.1_ASM2536381v1_genomic.fna/checkm_input GCA_025363815.1_ASM2536381v1_genomic.fna/checkm_result
[2023-06-30 12:05:33,477] [INFO] Task succeeded: CheckM
[2023-06-30 12:05:33,478] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 12:05:33,500] [INFO] ===== Completeness check finished =====
[2023-06-30 12:05:33,500] [INFO] ===== Start GTDB Search =====
[2023-06-30 12:05:33,500] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_025363815.1_ASM2536381v1_genomic.fna/markers.fasta)
[2023-06-30 12:05:33,501] [INFO] Task started: Blastn
[2023-06-30 12:05:33,501] [INFO] Running command: blastn -query GCA_025363815.1_ASM2536381v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd058ef51-4939-49f1-b8e3-c4c88730c366/dqc_reference/reference_markers_gtdb.fasta -out GCA_025363815.1_ASM2536381v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 12:05:34,519] [INFO] Task succeeded: Blastn
[2023-06-30 12:05:34,524] [INFO] Selected 18 target genomes.
[2023-06-30 12:05:34,524] [INFO] Target genome list was writen to GCA_025363815.1_ASM2536381v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 12:05:34,549] [INFO] Task started: fastANI
[2023-06-30 12:05:34,549] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e8714b0-82a2-4c6a-983a-8fedcd83e772/GCA_025363815.1_ASM2536381v1_genomic.fna.gz --refList GCA_025363815.1_ASM2536381v1_genomic.fna/target_genomes_gtdb.txt --output GCA_025363815.1_ASM2536381v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 12:05:44,706] [INFO] Task succeeded: fastANI
[2023-06-30 12:05:44,721] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 12:05:44,721] [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
GCA_016870395.1	s__SHUZ01 sp016870395	77.4721	251	863	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__IMCC26256;f__IMCC26256;g__SHUZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017882925.1	s__Chersky-534 sp017882925	77.3906	202	863	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__IMCC26256;f__Chersky-534;g__Chersky-534	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013695115.1	s__JACDBD01 sp013695115	77.322	155	863	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__IMCC26256;f__PALSA-555;g__JACDBD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016870245.1	s__CAIUKV01 sp016870245	77.2914	181	863	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__IMCC26256;f__PALSA-555;g__CAIUKV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016870595.1	s__CAIUKV01 sp016870595	77.0983	167	863	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__IMCC26256;f__PALSA-555;g__CAIUKV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017882945.1	s__Chersky-806 sp017882945	76.9838	226	863	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__IMCC26256;f__IMCC26256;g__Chersky-806	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903899845.1	s__CAIUKV01 sp903899845	76.8733	171	863	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__IMCC26256;f__PALSA-555;g__CAIUKV01	95.0	99.48	99.41	0.90	0.89	4	-
GCA_017853455.1	s__CAIUKV01 sp017853455	76.8664	135	863	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__IMCC26256;f__PALSA-555;g__CAIUKV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003140175.1	s__PALSA-555 sp003140175	76.8373	171	863	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__IMCC26256;f__PALSA-555;g__PALSA-555	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003134555.1	s__PALSA-610 sp003134555	76.6257	200	863	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__IMCC26256;f__PALSA-610;g__PALSA-610	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016650415.1	s__JAENVU01 sp016650415	76.6178	145	863	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__IMCC26256;f__IMCC26256;g__JAENVU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016185275.1	s__JACPNX01 sp016185275	76.0868	105	863	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JACPNX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003697065.1	s__J010 sp003697065	75.8907	72	863	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__J010	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364865.1	s__Ilumatobacter fluminis	75.751	95	863	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007713735.2	s__Amycolatopsis acidicola	74.8558	97	863	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 12:05:44,723] [INFO] GTDB search result was written to GCA_025363815.1_ASM2536381v1_genomic.fna/result_gtdb.tsv
[2023-06-30 12:05:44,723] [INFO] ===== GTDB Search completed =====
[2023-06-30 12:05:44,727] [INFO] DFAST_QC result json was written to GCA_025363815.1_ASM2536381v1_genomic.fna/dqc_result.json
[2023-06-30 12:05:44,727] [INFO] DFAST_QC completed!
[2023-06-30 12:05:44,728] [INFO] Total running time: 0h1m4s