[2024-01-24 11:59:06,307] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:06,309] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:06,309] [INFO] DQC Reference Directory: /var/lib/cwl/stg2a576921-439b-44d1-a671-476770cfb28d/dqc_reference
[2024-01-24 11:59:07,538] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:07,540] [INFO] Task started: Prodigal
[2024-01-24 11:59:07,540] [INFO] Running command: gunzip -c /var/lib/cwl/stg70da6bd1-09fa-4c18-b50c-93019ca08677/GCF_003352185.1_ASM335218v1_genomic.fna.gz | prodigal -d GCF_003352185.1_ASM335218v1_genomic.fna/cds.fna -a GCF_003352185.1_ASM335218v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:30,472] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:30,472] [INFO] Task started: HMMsearch
[2024-01-24 11:59:30,472] [INFO] Running command: hmmsearch --tblout GCF_003352185.1_ASM335218v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2a576921-439b-44d1-a671-476770cfb28d/dqc_reference/reference_markers.hmm GCF_003352185.1_ASM335218v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:30,899] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:30,900] [INFO] Found 6/6 markers.
[2024-01-24 11:59:30,956] [INFO] Query marker FASTA was written to GCF_003352185.1_ASM335218v1_genomic.fna/markers.fasta
[2024-01-24 11:59:30,957] [INFO] Task started: Blastn
[2024-01-24 11:59:30,957] [INFO] Running command: blastn -query GCF_003352185.1_ASM335218v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a576921-439b-44d1-a671-476770cfb28d/dqc_reference/reference_markers.fasta -out GCF_003352185.1_ASM335218v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:32,028] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:32,031] [INFO] Selected 16 target genomes.
[2024-01-24 11:59:32,031] [INFO] Target genome list was writen to GCF_003352185.1_ASM335218v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:32,037] [INFO] Task started: fastANI
[2024-01-24 11:59:32,037] [INFO] Running command: fastANI --query /var/lib/cwl/stg70da6bd1-09fa-4c18-b50c-93019ca08677/GCF_003352185.1_ASM335218v1_genomic.fna.gz --refList GCF_003352185.1_ASM335218v1_genomic.fna/target_genomes.txt --output GCF_003352185.1_ASM335218v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:58,379] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:58,379] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2a576921-439b-44d1-a671-476770cfb28d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:58,380] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2a576921-439b-44d1-a671-476770cfb28d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:58,393] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:59:58,393] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:58,393] [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
Pseudomonas kribbensis	strain=46-2	GCA_003352185.1	1628086	1628086	type	True	100.0	2104	2108	95	conclusive
Pseudomonas allokribbensis	strain=IzPS23	GCA_014863605.1	2774460	2774460	type	True	93.4285	1896	2108	95	below_threshold
Pseudomonas bananamidigenes	strain=BW11P2	GCA_001679645.1	2843610	2843610	type	True	92.1849	1739	2108	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	91.4595	1733	2108	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	91.3319	1675	2108	95	below_threshold
Pseudomonas koreensis	strain=DSM 16610	GCA_012986595.1	198620	198620	suspected-type	True	88.8817	1668	2108	95	below_threshold
Pseudomonas koreensis	strain=JCM 14769	GCA_014646955.1	198620	198620	suspected-type	True	88.8369	1680	2108	95	below_threshold
Pseudomonas koreensis	strain=CCUG 51519	GCA_008801535.1	198620	198620	suspected-type	True	88.8206	1671	2108	95	below_threshold
Pseudomonas monsensis	strain=PGSB 8459	GCA_014268495.2	2745509	2745509	type	True	88.4	1686	2108	95	below_threshold
Pseudomonas zeae	strain=OE 48.2	GCA_014268485.2	2745510	2745510	type	True	88.0779	1689	2108	95	below_threshold
Pseudomonas neuropathica	strain=P155	GCA_015461835.1	2730425	2730425	type	True	87.9576	1685	2108	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	87.9259	1685	2108	95	below_threshold
Pseudomonas granadensis	strain=LMG 27940	GCA_900105485.1	1421430	1421430	suspected-type	True	87.3106	1587	2108	95	below_threshold
Pseudomonas azerbaijanoriens	strain=SWRI123	GCA_019139795.1	2842350	2842350	type	True	86.4503	1433	2108	95	below_threshold
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	83.6472	1325	2108	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	83.581	1295	2108	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:58,395] [INFO] DFAST Taxonomy check result was written to GCF_003352185.1_ASM335218v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:58,396] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:58,396] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:58,396] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2a576921-439b-44d1-a671-476770cfb28d/dqc_reference/checkm_data
[2024-01-24 11:59:58,397] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:58,457] [INFO] Task started: CheckM
[2024-01-24 11:59:58,457] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003352185.1_ASM335218v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003352185.1_ASM335218v1_genomic.fna/checkm_input GCF_003352185.1_ASM335218v1_genomic.fna/checkm_result
[2024-01-24 12:01:13,200] [INFO] Task succeeded: CheckM
[2024-01-24 12:01:13,202] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:01:13,228] [INFO] ===== Completeness check finished =====
[2024-01-24 12:01:13,228] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:01:13,229] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003352185.1_ASM335218v1_genomic.fna/markers.fasta)
[2024-01-24 12:01:13,229] [INFO] Task started: Blastn
[2024-01-24 12:01:13,230] [INFO] Running command: blastn -query GCF_003352185.1_ASM335218v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a576921-439b-44d1-a671-476770cfb28d/dqc_reference/reference_markers_gtdb.fasta -out GCF_003352185.1_ASM335218v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:01:15,138] [INFO] Task succeeded: Blastn
[2024-01-24 12:01:15,143] [INFO] Selected 11 target genomes.
[2024-01-24 12:01:15,143] [INFO] Target genome list was writen to GCF_003352185.1_ASM335218v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:01:15,151] [INFO] Task started: fastANI
[2024-01-24 12:01:15,152] [INFO] Running command: fastANI --query /var/lib/cwl/stg70da6bd1-09fa-4c18-b50c-93019ca08677/GCF_003352185.1_ASM335218v1_genomic.fna.gz --refList GCF_003352185.1_ASM335218v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003352185.1_ASM335218v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:01:33,292] [INFO] Task succeeded: fastANI
[2024-01-24 12:01:33,302] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:01:33,302] [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_003352185.1	s__Pseudomonas_E kribbensis	100.0	2106	2108	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.22	95.68	0.92	0.89	10	conclusive
GCF_002112385.1	s__Pseudomonas_E sp002112385	94.1329	1834	2108	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	7	-
GCF_014863605.1	s__Pseudomonas_E allokribbensis	93.431	1897	2108	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.79	97.76	0.93	0.92	10	-
GCF_012974785.1	s__Pseudomonas_E fluorescens_BT	92.9631	1817	2108	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.87	98.87	0.96	0.96	2	-
GCF_004006335.1	s__Pseudomonas_E sp002112885	92.0126	1787	2108	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.01	95.48	0.92	0.90	14	-
GCF_003352875.1	s__Pseudomonas_E fluorescens_BF	91.9854	1826	2108	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014863585.1	s__Pseudomonas_E gozinkensis	91.8517	1795	2108	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010448615.1	s__Pseudomonas_E sp001655595	91.6966	1772	2108	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.61	96.24	0.94	0.90	22	-
GCF_002113125.1	s__Pseudomonas_E sp002113125	91.6063	1752	2108	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001594225.2	s__Pseudomonas_E glycinae	91.5136	1730	2108	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.56	95.98	0.93	0.88	9	-
GCF_002113045.1	s__Pseudomonas_E sp002113045	91.5042	1735	2108	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.93	98.93	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:01:33,304] [INFO] GTDB search result was written to GCF_003352185.1_ASM335218v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:01:33,305] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:01:33,312] [INFO] DFAST_QC result json was written to GCF_003352185.1_ASM335218v1_genomic.fna/dqc_result.json
[2024-01-24 12:01:33,312] [INFO] DFAST_QC completed!
[2024-01-24 12:01:33,312] [INFO] Total running time: 0h2m27s