[2024-01-24 12:21:36,135] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:36,137] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:36,138] [INFO] DQC Reference Directory: /var/lib/cwl/stga6610697-d04a-47ef-b2ea-9a582cf74fa3/dqc_reference
[2024-01-24 12:21:37,369] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:37,370] [INFO] Task started: Prodigal
[2024-01-24 12:21:37,371] [INFO] Running command: gunzip -c /var/lib/cwl/stg02c0bab8-b19d-433c-b713-0a0efb9dddc1/GCF_002906155.1_ASM290615v1_genomic.fna.gz | prodigal -d GCF_002906155.1_ASM290615v1_genomic.fna/cds.fna -a GCF_002906155.1_ASM290615v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:21:59,409] [INFO] Task succeeded: Prodigal
[2024-01-24 12:21:59,410] [INFO] Task started: HMMsearch
[2024-01-24 12:21:59,410] [INFO] Running command: hmmsearch --tblout GCF_002906155.1_ASM290615v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga6610697-d04a-47ef-b2ea-9a582cf74fa3/dqc_reference/reference_markers.hmm GCF_002906155.1_ASM290615v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:21:59,745] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:21:59,747] [INFO] Found 6/6 markers.
[2024-01-24 12:21:59,806] [INFO] Query marker FASTA was written to GCF_002906155.1_ASM290615v1_genomic.fna/markers.fasta
[2024-01-24 12:21:59,806] [INFO] Task started: Blastn
[2024-01-24 12:21:59,807] [INFO] Running command: blastn -query GCF_002906155.1_ASM290615v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga6610697-d04a-47ef-b2ea-9a582cf74fa3/dqc_reference/reference_markers.fasta -out GCF_002906155.1_ASM290615v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:00,753] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:00,757] [INFO] Selected 16 target genomes.
[2024-01-24 12:22:00,757] [INFO] Target genome list was writen to GCF_002906155.1_ASM290615v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:00,794] [INFO] Task started: fastANI
[2024-01-24 12:22:00,795] [INFO] Running command: fastANI --query /var/lib/cwl/stg02c0bab8-b19d-433c-b713-0a0efb9dddc1/GCF_002906155.1_ASM290615v1_genomic.fna.gz --refList GCF_002906155.1_ASM290615v1_genomic.fna/target_genomes.txt --output GCF_002906155.1_ASM290615v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:26,771] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:26,772] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga6610697-d04a-47ef-b2ea-9a582cf74fa3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:26,772] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga6610697-d04a-47ef-b2ea-9a582cf74fa3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:26,787] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:22:26,787] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:26,787] [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 laurylsulfativorans	strain=AP3_22	GCA_002906155.1	1943631	1943631	type	True	100.0	2215	2215	95	conclusive
Pseudomonas laurylsulfatiphila	strain=AP3_16	GCA_002934665.1	2011015	2011015	type	True	92.4458	1825	2215	95	below_threshold
Pseudomonas jessenii	strain=DSM 17150	GCA_002236115.1	77298	77298	suspected-type	True	92.3635	1743	2215	95	below_threshold
Pseudomonas azerbaijanoriens	strain=SWRI123	GCA_019139795.1	2842350	2842350	type	True	92.1935	1752	2215	95	below_threshold
Pseudomonas azerbaijanoccidens	strain=SWRI74	GCA_019145495.1	2842347	2842347	type	True	87.6887	1555	2215	95	below_threshold
Pseudomonas vancouverensis	strain=CCUG 49675	GCA_008801375.1	95300	95300	type	True	87.6674	1603	2215	95	below_threshold
Pseudomonas reinekei	strain=CCUG 53116	GCA_008801455.1	395598	395598	type	True	87.5394	1479	2215	95	below_threshold
Pseudomonas reinekei	strain=MT1	GCA_001945365.1	395598	395598	type	True	87.5249	1480	2215	95	below_threshold
Pseudomonas izuensis	strain=IzPS43_3003	GCA_009861505.1	2684212	2684212	type	True	87.455	1585	2215	95	below_threshold
Pseudomonas moorei	strain=CCUG 53114	GCA_008801475.1	395599	395599	type	True	87.356	1556	2215	95	below_threshold
Pseudomonas farris	strain=SWRI79	GCA_019145235.1	2841207	2841207	type	True	86.5963	1418	2215	95	below_threshold
Pseudomonas kribbensis	strain=46-2	GCA_003352185.1	1628086	1628086	type	True	86.2729	1430	2215	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	86.2462	1416	2215	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	86.0689	1386	2215	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	85.4579	1413	2215	95	below_threshold
Pseudomonas brassicae	strain=MAFF 212427	GCA_010671725.1	2708063	2708063	type	True	81.8796	841	2215	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:26,789] [INFO] DFAST Taxonomy check result was written to GCF_002906155.1_ASM290615v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:26,790] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:26,790] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:26,790] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga6610697-d04a-47ef-b2ea-9a582cf74fa3/dqc_reference/checkm_data
[2024-01-24 12:22:26,791] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:26,856] [INFO] Task started: CheckM
[2024-01-24 12:22:26,857] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002906155.1_ASM290615v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002906155.1_ASM290615v1_genomic.fna/checkm_input GCF_002906155.1_ASM290615v1_genomic.fna/checkm_result
[2024-01-24 12:23:30,577] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:30,579] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:30,606] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:30,606] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:30,607] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002906155.1_ASM290615v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:30,607] [INFO] Task started: Blastn
[2024-01-24 12:23:30,608] [INFO] Running command: blastn -query GCF_002906155.1_ASM290615v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga6610697-d04a-47ef-b2ea-9a582cf74fa3/dqc_reference/reference_markers_gtdb.fasta -out GCF_002906155.1_ASM290615v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:32,335] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:32,338] [INFO] Selected 14 target genomes.
[2024-01-24 12:23:32,339] [INFO] Target genome list was writen to GCF_002906155.1_ASM290615v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:32,350] [INFO] Task started: fastANI
[2024-01-24 12:23:32,350] [INFO] Running command: fastANI --query /var/lib/cwl/stg02c0bab8-b19d-433c-b713-0a0efb9dddc1/GCF_002906155.1_ASM290615v1_genomic.fna.gz --refList GCF_002906155.1_ASM290615v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002906155.1_ASM290615v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:57,308] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:57,320] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:57,321] [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_002906155.1	s__Pseudomonas_E laurylsulfativorans	100.0	2215	2215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002113375.1	s__Pseudomonas_E sp002113375	93.8043	1693	2215	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_009764265.1	s__Pseudomonas_E sp009764265	92.5154	1779	2215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.48	95.48	0.85	0.85	2	-
GCF_902498135.1	s__Pseudomonas_E fluorescens_BH	92.4811	1699	2215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.39	98.07	0.87	0.86	3	-
GCF_000967965.1	s__Pseudomonas_E fluorescens_O	92.4711	1711	2215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.01	99.01	0.96	0.96	2	-
GCF_002934665.1	s__Pseudomonas_E laurylsulfatiphila	92.437	1826	2215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.04	95.74	0.86	0.82	13	-
GCF_002236115.1	s__Pseudomonas_E jessenii	92.3635	1743	2215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.88	96.89	0.89	0.84	18	-
GCF_000282455.1	s__Pseudomonas_E sp000282455	92.2699	1620	2215	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_002303925.1	s__Pseudomonas_E sp002303925	92.2019	1666	2215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.04	99.04	0.91	0.91	2	-
GCF_003050925.1	s__Pseudomonas_E sp003050925	92.1759	1660	2215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.23	96.92	0.93	0.89	3	-
GCF_003053605.1	s__Pseudomonas_E sp003053605	92.0318	1678	2215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.75	96.54	0.88	0.80	4	-
GCF_016909445.1	s__Pseudomonas_E stutzeri_A	91.8794	1667	2215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.88	96.88	0.84	0.84	2	-
GCF_002113025.1	s__Pseudomonas_E sp002113025	91.8483	1676	2215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.31	95.23	0.87	0.84	4	-
GCF_001269805.1	s__Pseudomonas_E sp001269805	88.0596	1564	2215	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:57,323] [INFO] GTDB search result was written to GCF_002906155.1_ASM290615v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:57,323] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:57,327] [INFO] DFAST_QC result json was written to GCF_002906155.1_ASM290615v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:57,327] [INFO] DFAST_QC completed!
[2024-01-24 12:23:57,327] [INFO] Total running time: 0h2m21s