[2023-06-30 01:58:02,835] [INFO] DFAST_QC pipeline started.
[2023-06-30 01:58:02,838] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 01:58:02,838] [INFO] DQC Reference Directory: /var/lib/cwl/stgd76b01c3-6775-4eea-ac72-9b789a5a2ab7/dqc_reference
[2023-06-30 01:58:04,157] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 01:58:04,159] [INFO] Task started: Prodigal
[2023-06-30 01:58:04,159] [INFO] Running command: gunzip -c /var/lib/cwl/stg330124cc-0eb2-4467-81aa-f3f8ca06afa7/GCA_016708695.1_ASM1670869v1_genomic.fna.gz | prodigal -d GCA_016708695.1_ASM1670869v1_genomic.fna/cds.fna -a GCA_016708695.1_ASM1670869v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 01:58:18,715] [INFO] Task succeeded: Prodigal
[2023-06-30 01:58:18,716] [INFO] Task started: HMMsearch
[2023-06-30 01:58:18,716] [INFO] Running command: hmmsearch --tblout GCA_016708695.1_ASM1670869v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd76b01c3-6775-4eea-ac72-9b789a5a2ab7/dqc_reference/reference_markers.hmm GCA_016708695.1_ASM1670869v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 01:58:19,016] [INFO] Task succeeded: HMMsearch
[2023-06-30 01:58:19,017] [INFO] Found 6/6 markers.
[2023-06-30 01:58:19,058] [INFO] Query marker FASTA was written to GCA_016708695.1_ASM1670869v1_genomic.fna/markers.fasta
[2023-06-30 01:58:19,058] [INFO] Task started: Blastn
[2023-06-30 01:58:19,058] [INFO] Running command: blastn -query GCA_016708695.1_ASM1670869v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd76b01c3-6775-4eea-ac72-9b789a5a2ab7/dqc_reference/reference_markers.fasta -out GCA_016708695.1_ASM1670869v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 01:58:19,746] [INFO] Task succeeded: Blastn
[2023-06-30 01:58:19,752] [INFO] Selected 26 target genomes.
[2023-06-30 01:58:19,752] [INFO] Target genome list was writen to GCA_016708695.1_ASM1670869v1_genomic.fna/target_genomes.txt
[2023-06-30 01:58:19,754] [INFO] Task started: fastANI
[2023-06-30 01:58:19,755] [INFO] Running command: fastANI --query /var/lib/cwl/stg330124cc-0eb2-4467-81aa-f3f8ca06afa7/GCA_016708695.1_ASM1670869v1_genomic.fna.gz --refList GCA_016708695.1_ASM1670869v1_genomic.fna/target_genomes.txt --output GCA_016708695.1_ASM1670869v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 01:58:37,249] [INFO] Task succeeded: fastANI
[2023-06-30 01:58:37,250] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd76b01c3-6775-4eea-ac72-9b789a5a2ab7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 01:58:37,250] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd76b01c3-6775-4eea-ac72-9b789a5a2ab7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 01:58:37,262] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 01:58:37,262] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 01:58:37,262] [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
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	76.5292	167	1429	95	below_threshold
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	76.3912	112	1429	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	76.3016	189	1429	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	76.201	140	1429	95	below_threshold
Ilumatobacter nonamiensis	strain=YM16-303	GCA_000350145.1	467093	467093	type	True	76.1317	96	1429	95	below_threshold
Motilibacter peucedani	strain=RP-AC37	GCA_003634695.1	598650	598650	type	True	75.5692	96	1429	95	below_threshold
Motilibacter rhizosphaerae	strain=DSM 45622	GCA_004216915.1	598652	598652	type	True	75.5589	81	1429	95	below_threshold
Nitriliruptor alkaliphilus	strain=DSM 45188	GCA_000969705.1	427918	427918	type	True	75.4902	96	1429	95	below_threshold
Euzebya rosea	strain=DSW09	GCA_003073135.1	2052804	2052804	type	True	75.3576	90	1429	95	below_threshold
Streptosporangium becharense	strain=CECT 8961	GCA_014191075.1	1816182	1816182	type	True	75.3473	107	1429	95	below_threshold
Streptomonospora litoralis	strain=M2	GCA_004323735.1	2498135	2498135	type	True	75.3033	99	1429	95	below_threshold
Nocardiopsis potens	strain=DSM 45234	GCA_000341105.1	1246458	1246458	type	True	75.2612	125	1429	95	below_threshold
Hydrogenophaga borbori	strain=LA-38	GCA_003417535.1	2294117	2294117	type	True	75.1281	53	1429	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 01:58:37,265] [INFO] DFAST Taxonomy check result was written to GCA_016708695.1_ASM1670869v1_genomic.fna/tc_result.tsv
[2023-06-30 01:58:37,266] [INFO] ===== Taxonomy check completed =====
[2023-06-30 01:58:37,266] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 01:58:37,266] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd76b01c3-6775-4eea-ac72-9b789a5a2ab7/dqc_reference/checkm_data
[2023-06-30 01:58:37,268] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 01:58:37,320] [INFO] Task started: CheckM
[2023-06-30 01:58:37,321] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016708695.1_ASM1670869v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016708695.1_ASM1670869v1_genomic.fna/checkm_input GCA_016708695.1_ASM1670869v1_genomic.fna/checkm_result
[2023-06-30 01:59:37,526] [INFO] Task succeeded: CheckM
[2023-06-30 01:59:37,528] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 01:59:37,550] [INFO] ===== Completeness check finished =====
[2023-06-30 01:59:37,551] [INFO] ===== Start GTDB Search =====
[2023-06-30 01:59:37,551] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016708695.1_ASM1670869v1_genomic.fna/markers.fasta)
[2023-06-30 01:59:37,551] [INFO] Task started: Blastn
[2023-06-30 01:59:37,552] [INFO] Running command: blastn -query GCA_016708695.1_ASM1670869v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd76b01c3-6775-4eea-ac72-9b789a5a2ab7/dqc_reference/reference_markers_gtdb.fasta -out GCA_016708695.1_ASM1670869v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 01:59:38,441] [INFO] Task succeeded: Blastn
[2023-06-30 01:59:38,446] [INFO] Selected 17 target genomes.
[2023-06-30 01:59:38,447] [INFO] Target genome list was writen to GCA_016708695.1_ASM1670869v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 01:59:38,451] [INFO] Task started: fastANI
[2023-06-30 01:59:38,451] [INFO] Running command: fastANI --query /var/lib/cwl/stg330124cc-0eb2-4467-81aa-f3f8ca06afa7/GCA_016708695.1_ASM1670869v1_genomic.fna.gz --refList GCA_016708695.1_ASM1670869v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016708695.1_ASM1670869v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 01:59:49,122] [INFO] Task succeeded: fastANI
[2023-06-30 01:59:49,137] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 01:59:49,137] [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_000299415.1	s__Microthrix parvicella	98.9172	1252	1429	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__Microthrix	95.0	99.08	98.57	0.94	0.83	22	conclusive
GCA_016719385.1	s__Microthrix sp002473265	81.5263	799	1429	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__Microthrix	95.0	98.81	98.46	0.90	0.86	7	-
GCA_903941145.1	s__CAJANQ01 sp903941145	76.9301	101	1429	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__CAJANQ01	95.0	98.35	98.35	0.80	0.80	2	-
GCA_016703525.1	s__JADJBW01 sp016703525	76.6791	168	1429	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__JADJBW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903873135.1	s__SXMI01 sp903873135	76.5479	143	1429	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__SXMI01	95.0	99.54	99.49	0.91	0.89	9	-
GCA_007118345.1	s__SKRR01 sp007118345	76.5249	131	1429	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__SKRR01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009650215.1	s__Actinomarinicola tropica	76.5175	168	1429	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SKKL01;g__Actinomarinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903868545.1	s__CAIPVR01 sp903868545	76.4347	182	1429	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__CAIPVR01	95.0	99.51	99.50	0.87	0.86	3	-
GCA_009844405.1	s__VYCW01 sp009844405	76.2503	107	1429	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__VYCW01	95.0	99.44	99.17	0.93	0.90	7	-
GCA_903925745.1	s__SXMI01 sp903925745	76.1604	124	1429	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__SXMI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826025.1	s__CADEDH01 sp902826025	76.0287	202	1429	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SZUA-35;g__CADEDH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013694495.1	s__JACDCH01 sp013694495	76.0142	123	1429	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JACDCH01;g__JACDCH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805655.1	s__CADCTF01 sp902805655	75.9534	104	1429	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__CADCTF01;g__CADCTF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003073135.1	s__Euzebya rosea	75.3667	89	1429	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Euzebyaceae;g__Euzebya	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 01:59:49,139] [INFO] GTDB search result was written to GCA_016708695.1_ASM1670869v1_genomic.fna/result_gtdb.tsv
[2023-06-30 01:59:49,140] [INFO] ===== GTDB Search completed =====
[2023-06-30 01:59:49,144] [INFO] DFAST_QC result json was written to GCA_016708695.1_ASM1670869v1_genomic.fna/dqc_result.json
[2023-06-30 01:59:49,144] [INFO] DFAST_QC completed!
[2023-06-30 01:59:49,144] [INFO] Total running time: 0h1m46s