[2024-01-24 13:57:56,093] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:56,095] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:56,095] [INFO] DQC Reference Directory: /var/lib/cwl/stg0c3abfe4-b4ec-4d56-9edd-0e67cf10fe46/dqc_reference
[2024-01-24 13:57:57,493] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:57,496] [INFO] Task started: Prodigal
[2024-01-24 13:57:57,497] [INFO] Running command: gunzip -c /var/lib/cwl/stge730962d-dbcb-4cda-94cd-f171d17b48cb/GCF_004521985.1_ASM452198v1_genomic.fna.gz | prodigal -d GCF_004521985.1_ASM452198v1_genomic.fna/cds.fna -a GCF_004521985.1_ASM452198v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:14,109] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:14,110] [INFO] Task started: HMMsearch
[2024-01-24 13:58:14,110] [INFO] Running command: hmmsearch --tblout GCF_004521985.1_ASM452198v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0c3abfe4-b4ec-4d56-9edd-0e67cf10fe46/dqc_reference/reference_markers.hmm GCF_004521985.1_ASM452198v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:14,440] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:14,442] [INFO] Found 6/6 markers.
[2024-01-24 13:58:14,496] [INFO] Query marker FASTA was written to GCF_004521985.1_ASM452198v1_genomic.fna/markers.fasta
[2024-01-24 13:58:14,496] [INFO] Task started: Blastn
[2024-01-24 13:58:14,496] [INFO] Running command: blastn -query GCF_004521985.1_ASM452198v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c3abfe4-b4ec-4d56-9edd-0e67cf10fe46/dqc_reference/reference_markers.fasta -out GCF_004521985.1_ASM452198v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:15,750] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:15,754] [INFO] Selected 17 target genomes.
[2024-01-24 13:58:15,754] [INFO] Target genome list was writen to GCF_004521985.1_ASM452198v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:15,761] [INFO] Task started: fastANI
[2024-01-24 13:58:15,762] [INFO] Running command: fastANI --query /var/lib/cwl/stge730962d-dbcb-4cda-94cd-f171d17b48cb/GCF_004521985.1_ASM452198v1_genomic.fna.gz --refList GCF_004521985.1_ASM452198v1_genomic.fna/target_genomes.txt --output GCF_004521985.1_ASM452198v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:37,541] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:37,542] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0c3abfe4-b4ec-4d56-9edd-0e67cf10fe46/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:37,542] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0c3abfe4-b4ec-4d56-9edd-0e67cf10fe46/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:37,559] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:58:37,559] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:58:37,559] [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 guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	88.0904	1331	1715	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	88.0322	1268	1715	95	below_threshold
Pseudomonas chengduensis	strain=MBR	GCA_017905455.1	489632	489632	type	True	87.742	1325	1715	95	below_threshold
Pseudomonas chengduensis	strain=DSM 26382	GCA_012986985.1	489632	489632	type	True	87.7371	1331	1715	95	below_threshold
Pseudomonas alcaliphila	strain=JCM 10630	GCA_900101755.1	101564	101564	type	True	87.6625	1350	1715	95	below_threshold
Pseudomonas alcaliphila	strain=NBRC 102411	GCA_002091495.1	101564	101564	type	True	87.6218	1356	1715	95	below_threshold
Pseudomonas toyotomiensis	strain=DSM 26169	GCA_002741095.1	554344	554344	type	True	87.6197	1341	1715	95	below_threshold
Pseudomonas toyotomiensis	strain=JCM 15604	GCA_900115695.1	554344	554344	type	True	87.5903	1345	1715	95	below_threshold
Pseudomonas sihuiensis	strain=KCTC 32246	GCA_900106015.1	1274359	1274359	type	True	87.5749	1329	1715	95	below_threshold
Pseudomonas yangonensis	strain=MY50	GCA_009932725.1	2579922	2579922	type	True	87.5469	1249	1715	95	below_threshold
Pseudomonas composti	strain=CCUG 59231	GCA_900115475.1	658457	658457	type	True	87.4629	1403	1715	95	below_threshold
Pseudomonas sediminis	strain=PI11	GCA_002741105.1	1691904	1691904	type	True	87.3532	1325	1715	95	below_threshold
Pseudomonas oleovorans subsp. oleovorans	strain=NBRC 13583	GCA_002091815.1	1218129	301	type	True	87.3015	1130	1715	95	below_threshold
Pseudomonas mendocina	strain=NCTC10897	GCA_900636545.1	300	300	suspected-type	True	87.2322	1337	1715	95	below_threshold
Pseudomonas mendocina	strain=NBRC 14162	GCA_000813265.1	300	300	suspected-type	True	87.2222	1316	1715	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	84.2365	1001	1715	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	82.8116	942	1715	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:37,561] [INFO] DFAST Taxonomy check result was written to GCF_004521985.1_ASM452198v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:37,562] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:37,562] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:37,562] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0c3abfe4-b4ec-4d56-9edd-0e67cf10fe46/dqc_reference/checkm_data
[2024-01-24 13:58:37,563] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:37,621] [INFO] Task started: CheckM
[2024-01-24 13:58:37,621] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004521985.1_ASM452198v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004521985.1_ASM452198v1_genomic.fna/checkm_input GCF_004521985.1_ASM452198v1_genomic.fna/checkm_result
[2024-01-24 13:59:25,970] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:25,971] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:25,994] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:25,994] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:25,995] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004521985.1_ASM452198v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:25,995] [INFO] Task started: Blastn
[2024-01-24 13:59:25,995] [INFO] Running command: blastn -query GCF_004521985.1_ASM452198v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c3abfe4-b4ec-4d56-9edd-0e67cf10fe46/dqc_reference/reference_markers_gtdb.fasta -out GCF_004521985.1_ASM452198v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:28,177] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:28,181] [INFO] Selected 16 target genomes.
[2024-01-24 13:59:28,181] [INFO] Target genome list was writen to GCF_004521985.1_ASM452198v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:28,261] [INFO] Task started: fastANI
[2024-01-24 13:59:28,261] [INFO] Running command: fastANI --query /var/lib/cwl/stge730962d-dbcb-4cda-94cd-f171d17b48cb/GCF_004521985.1_ASM452198v1_genomic.fna.gz --refList GCF_004521985.1_ASM452198v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004521985.1_ASM452198v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:47,912] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:47,931] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:47,932] [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_004521985.1	s__Pseudomonas_E khazarica	100.0	1713	1715	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.35	98.01	0.91	0.87	12	conclusive
GCF_900104265.1	s__Pseudomonas_E guguanensis	88.1108	1328	1715	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.13	97.13	0.85	0.85	2	-
GCF_000016565.1	s__Pseudomonas_E mendocina_A	87.9427	1298	1715	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.76	97.37	0.90	0.88	7	-
GCF_002803095.1	s__Pseudomonas_E sp002803095	87.785	1309	1715	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.6432	99.96	99.96	0.99	0.99	2	-
GCF_900101755.1	s__Pseudomonas_E alcaliphila	87.6624	1350	1715	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.74	97.49	0.95	0.92	3	-
GCF_001941865.1	s__Pseudomonas_E alcaliphila_B	87.6602	1296	1715	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.7502	96.52	96.24	0.87	0.86	3	-
GCF_000418555.1	s__Pseudomonas_E sp000418555	87.6371	1295	1715	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_900115695.1	s__Pseudomonas_E toyotomiensis	87.6097	1343	1715	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.1942	98.17	97.23	0.91	0.85	7	-
GCF_003696305.1	s__Pseudomonas_E sp003696305	87.5973	1190	1715	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_900106015.1	s__Pseudomonas_E sihuiensis	87.575	1329	1715	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	96.7402	N/A	N/A	N/A	N/A	1	-
GCF_009932725.1	s__Pseudomonas_E sp009932725	87.526	1251	1715	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.40	98.35	0.94	0.88	4	-
GCF_016008875.1	s__Pseudomonas_E sp002439135	87.5045	1269	1715	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.91	96.75	0.87	0.85	5	-
GCF_002741105.1	s__Pseudomonas_E sediminis	87.3369	1327	1715	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.01	95.51	0.89	0.85	6	-
GCF_900636545.1	s__Pseudomonas_E mendocina	87.2418	1336	1715	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.91	97.19	0.93	0.89	14	-
GCF_007049795.1	s__Pseudomonas_E mendocina_D	87.224	1230	1715	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.17	96.47	0.87	0.84	6	-
GCF_014109765.1	s__Pseudomonas_E oleovorans_B	86.5784	1341	1715	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.92	96.88	0.93	0.92	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:47,934] [INFO] GTDB search result was written to GCF_004521985.1_ASM452198v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:47,934] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:47,939] [INFO] DFAST_QC result json was written to GCF_004521985.1_ASM452198v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:47,939] [INFO] DFAST_QC completed!
[2024-01-24 13:59:47,939] [INFO] Total running time: 0h1m52s