[2024-01-24 15:18:38,692] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:38,694] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:38,694] [INFO] DQC Reference Directory: /var/lib/cwl/stg3a6c6ed2-a997-4461-9133-83dfd4167135/dqc_reference
[2024-01-24 15:18:39,943] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:39,944] [INFO] Task started: Prodigal
[2024-01-24 15:18:39,944] [INFO] Running command: gunzip -c /var/lib/cwl/stg89ca9c82-118f-435d-b519-bcb7d2cdfff8/GCF_002236105.1_ASM223610v1_genomic.fna.gz | prodigal -d GCF_002236105.1_ASM223610v1_genomic.fna/cds.fna -a GCF_002236105.1_ASM223610v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:19:05,719] [INFO] Task succeeded: Prodigal
[2024-01-24 15:19:05,720] [INFO] Task started: HMMsearch
[2024-01-24 15:19:05,720] [INFO] Running command: hmmsearch --tblout GCF_002236105.1_ASM223610v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3a6c6ed2-a997-4461-9133-83dfd4167135/dqc_reference/reference_markers.hmm GCF_002236105.1_ASM223610v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:19:06,136] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:19:06,138] [INFO] Found 6/6 markers.
[2024-01-24 15:19:06,204] [INFO] Query marker FASTA was written to GCF_002236105.1_ASM223610v1_genomic.fna/markers.fasta
[2024-01-24 15:19:06,205] [INFO] Task started: Blastn
[2024-01-24 15:19:06,205] [INFO] Running command: blastn -query GCF_002236105.1_ASM223610v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a6c6ed2-a997-4461-9133-83dfd4167135/dqc_reference/reference_markers.fasta -out GCF_002236105.1_ASM223610v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:07,261] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:07,265] [INFO] Selected 19 target genomes.
[2024-01-24 15:19:07,266] [INFO] Target genome list was writen to GCF_002236105.1_ASM223610v1_genomic.fna/target_genomes.txt
[2024-01-24 15:19:07,273] [INFO] Task started: fastANI
[2024-01-24 15:19:07,274] [INFO] Running command: fastANI --query /var/lib/cwl/stg89ca9c82-118f-435d-b519-bcb7d2cdfff8/GCF_002236105.1_ASM223610v1_genomic.fna.gz --refList GCF_002236105.1_ASM223610v1_genomic.fna/target_genomes.txt --output GCF_002236105.1_ASM223610v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:42,204] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:42,205] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3a6c6ed2-a997-4461-9133-83dfd4167135/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:42,206] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3a6c6ed2-a997-4461-9133-83dfd4167135/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:42,223] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:19:42,223] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:42,224] [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 umsongensis	strain=DSM 16611	GCA_002236105.1	198618	198618	type	True	100.0	2225	2227	95	conclusive
Pseudomonas izuensis	strain=IzPS43_3003	GCA_009861505.1	2684212	2684212	type	True	87.6236	1590	2227	95	below_threshold
Pseudomonas azerbaijanoccidens	strain=SWRI74	GCA_019145495.1	2842347	2842347	type	True	87.3675	1550	2227	95	below_threshold
Pseudomonas reinekei	strain=CCUG 53116	GCA_008801455.1	395598	395598	type	True	87.2677	1518	2227	95	below_threshold
Pseudomonas reinekei	strain=MT1	GCA_001945365.1	395598	395598	type	True	87.2453	1516	2227	95	below_threshold
Pseudomonas jessenii	strain=DSM 17150	GCA_002236115.1	77298	77298	suspected-type	True	87.233	1544	2227	95	below_threshold
Pseudomonas laurylsulfatiphila	strain=AP3_16	GCA_002934665.1	2011015	2011015	type	True	87.1585	1573	2227	95	below_threshold
Pseudomonas moorei	strain=CCUG 53114	GCA_008801475.1	395599	395599	type	True	87.1053	1584	2227	95	below_threshold
Pseudomonas azerbaijanoriens	strain=SWRI123	GCA_019139795.1	2842350	2842350	type	True	87.0947	1569	2227	95	below_threshold
Pseudomonas laurylsulfativorans	strain=AP3_22	GCA_002906155.1	1943631	1943631	type	True	87.0107	1572	2227	95	below_threshold
Pseudomonas mohnii	strain=DSM 18327	GCA_900105115.1	395600	395600	type	True	86.9753	1606	2227	95	below_threshold
Pseudomonas lini	strain=DSM 16768	GCA_001042905.1	163011	163011	type	True	86.2434	1384	2227	95	below_threshold
Pseudomonas mandelii	strain=NBRC 103147	GCA_002091695.1	75612	75612	suspected-type	True	86.2313	1521	2227	95	below_threshold
Pseudomonas lini	strain=CCUG 51522	GCA_008801525.1	163011	163011	type	True	86.1932	1407	2227	95	below_threshold
Pseudomonas farris	strain=SWRI79	GCA_019145235.1	2841207	2841207	type	True	86.1427	1408	2227	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	85.5287	1377	2227	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	85.4081	1361	2227	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	84.9301	1348	2227	95	below_threshold
Pseudomonas brassicae	strain=MAFF 212427	GCA_010671725.1	2708063	2708063	type	True	81.9803	831	2227	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:42,225] [INFO] DFAST Taxonomy check result was written to GCF_002236105.1_ASM223610v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:42,226] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:42,226] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:42,226] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3a6c6ed2-a997-4461-9133-83dfd4167135/dqc_reference/checkm_data
[2024-01-24 15:19:42,227] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:42,292] [INFO] Task started: CheckM
[2024-01-24 15:19:42,292] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002236105.1_ASM223610v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002236105.1_ASM223610v1_genomic.fna/checkm_input GCF_002236105.1_ASM223610v1_genomic.fna/checkm_result
[2024-01-24 15:20:54,882] [INFO] Task succeeded: CheckM
[2024-01-24 15:20:54,884] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:20:54,913] [INFO] ===== Completeness check finished =====
[2024-01-24 15:20:54,913] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:20:54,914] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002236105.1_ASM223610v1_genomic.fna/markers.fasta)
[2024-01-24 15:20:54,914] [INFO] Task started: Blastn
[2024-01-24 15:20:54,914] [INFO] Running command: blastn -query GCF_002236105.1_ASM223610v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a6c6ed2-a997-4461-9133-83dfd4167135/dqc_reference/reference_markers_gtdb.fasta -out GCF_002236105.1_ASM223610v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:20:56,615] [INFO] Task succeeded: Blastn
[2024-01-24 15:20:56,622] [INFO] Selected 15 target genomes.
[2024-01-24 15:20:56,622] [INFO] Target genome list was writen to GCF_002236105.1_ASM223610v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:20:56,655] [INFO] Task started: fastANI
[2024-01-24 15:20:56,655] [INFO] Running command: fastANI --query /var/lib/cwl/stg89ca9c82-118f-435d-b519-bcb7d2cdfff8/GCF_002236105.1_ASM223610v1_genomic.fna.gz --refList GCF_002236105.1_ASM223610v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002236105.1_ASM223610v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:21:26,401] [INFO] Task succeeded: fastANI
[2024-01-24 15:21:26,418] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:21:26,419] [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_002236105.1	s__Pseudomonas_E umsongensis	100.0	2225	2227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.47	96.72	0.91	0.86	9	conclusive
GCF_000282475.1	s__Pseudomonas_E sp000282475	92.6576	1751	2227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.45	95.45	0.83	0.83	2	-
GCF_001976065.1	s__Pseudomonas_E putida_G	90.7039	1817	2227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.27	99.27	0.91	0.91	2	-
GCF_902498195.1	s__Pseudomonas_E fluorescens_BU	87.9035	1646	2227	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_000802965.1	s__Pseudomonas_E fluorescens_A	87.8731	1562	2227	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_013359695.1	s__Pseudomonas_E sp013359695	87.7846	1567	2227	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_902497845.1	s__Pseudomonas_E fluorescens_BN	87.3231	1558	2227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.81	98.81	0.91	0.91	2	-
GCF_001945365.1	s__Pseudomonas_E reinekei	87.2587	1514	2227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.76	95.43	0.93	0.85	5	-
GCF_002236115.1	s__Pseudomonas_E jessenii	87.2052	1548	2227	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_001984065.1	s__Pseudomonas_E sp001984065	87.0596	1475	2227	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_001427125.1	s__Pseudomonas_E sp001427125	86.973	1542	2227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.98	98.83	0.91	0.89	5	-
GCF_003050925.1	s__Pseudomonas_E sp003050925	86.9226	1500	2227	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_000968015.1	s__Pseudomonas_E fluorescens_W	86.5071	1521	2227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.19	96.19	0.86	0.86	2	-
GCF_001661075.1	s__Pseudomonas_E silesiensis	86.3889	1568	2227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.70	96.64	0.87	0.85	5	-
GCF_006094435.1	s__Pseudomonas_E sp002029345	86.3266	1609	2227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.75	98.73	0.83	0.83	3	-
--------------------------------------------------------------------------------
[2024-01-24 15:21:26,425] [INFO] GTDB search result was written to GCF_002236105.1_ASM223610v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:21:26,426] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:21:26,433] [INFO] DFAST_QC result json was written to GCF_002236105.1_ASM223610v1_genomic.fna/dqc_result.json
[2024-01-24 15:21:26,434] [INFO] DFAST_QC completed!
[2024-01-24 15:21:26,434] [INFO] Total running time: 0h2m48s