[2024-01-24 13:48:59,838] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:59,841] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:59,841] [INFO] DQC Reference Directory: /var/lib/cwl/stg4f51b7a6-1d0f-4f05-8bd9-98c5c1d44f99/dqc_reference
[2024-01-24 13:49:01,111] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:01,112] [INFO] Task started: Prodigal
[2024-01-24 13:49:01,112] [INFO] Running command: gunzip -c /var/lib/cwl/stgdc7a28fc-69ec-464f-b8de-23e6360d7cd6/GCF_007109405.1_ASM710940v1_genomic.fna.gz | prodigal -d GCF_007109405.1_ASM710940v1_genomic.fna/cds.fna -a GCF_007109405.1_ASM710940v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:15,475] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:15,476] [INFO] Task started: HMMsearch
[2024-01-24 13:49:15,476] [INFO] Running command: hmmsearch --tblout GCF_007109405.1_ASM710940v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4f51b7a6-1d0f-4f05-8bd9-98c5c1d44f99/dqc_reference/reference_markers.hmm GCF_007109405.1_ASM710940v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:15,809] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:15,810] [INFO] Found 6/6 markers.
[2024-01-24 13:49:15,849] [INFO] Query marker FASTA was written to GCF_007109405.1_ASM710940v1_genomic.fna/markers.fasta
[2024-01-24 13:49:15,849] [INFO] Task started: Blastn
[2024-01-24 13:49:15,849] [INFO] Running command: blastn -query GCF_007109405.1_ASM710940v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f51b7a6-1d0f-4f05-8bd9-98c5c1d44f99/dqc_reference/reference_markers.fasta -out GCF_007109405.1_ASM710940v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:16,834] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:16,837] [INFO] Selected 23 target genomes.
[2024-01-24 13:49:16,838] [INFO] Target genome list was writen to GCF_007109405.1_ASM710940v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:16,846] [INFO] Task started: fastANI
[2024-01-24 13:49:16,846] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc7a28fc-69ec-464f-b8de-23e6360d7cd6/GCF_007109405.1_ASM710940v1_genomic.fna.gz --refList GCF_007109405.1_ASM710940v1_genomic.fna/target_genomes.txt --output GCF_007109405.1_ASM710940v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:44,305] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:44,305] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4f51b7a6-1d0f-4f05-8bd9-98c5c1d44f99/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:44,306] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4f51b7a6-1d0f-4f05-8bd9-98c5c1d44f99/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:44,323] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:44,324] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:44,324] [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 mangiferae	strain=DMKU BBB3-04	GCA_007109405.1	2593654	2593654	type	True	100.0	1540	1540	95	conclusive
Pseudomonas tohonis	strain=TUM18999	GCA_012767755.2	2725477	2725477	type	True	83.2463	1043	1540	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	83.1376	821	1540	95	below_threshold
Pseudomonas delhiensis	strain=RLD-1	GCA_900187975.1	366289	366289	type	True	83.0917	981	1540	95	below_threshold
Pseudomonas delhiensis	strain=CCM 7361	GCA_900099945.1	366289	366289	type	True	83.0215	996	1540	95	below_threshold
Pseudomonas citronellolis	strain=DSM 50332	GCA_004745455.1	53408	53408	type	True	82.9274	997	1540	95	below_threshold
Pseudomonas citronellolis	strain=NBRC 103043	GCA_002091555.1	53408	53408	type	True	82.9001	986	1540	95	below_threshold
Pseudomonas citronellolis	strain=LMG 18378	GCA_900112375.1	53408	53408	type	True	82.8876	985	1540	95	below_threshold
Pseudomonas furukawaii	strain=KF707	GCA_002355475.1	1149133	1149133	type	True	82.608	887	1540	95	below_threshold
Pseudomonas furukawaii	strain=KF707	GCA_000262065.3	1149133	1149133	type	True	82.5387	897	1540	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	82.2813	824	1540	95	below_threshold
Pseudomonas kuykendallii	strain=NRRL B-59562	GCA_900106975.1	1007099	1007099	type	True	82.2212	867	1540	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	82.1229	633	1540	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	82.0641	862	1540	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_900167195.1	287	287	type	True	82.0555	943	1540	95	below_threshold
Pseudomonas linyingensis	strain=LMG 25967	GCA_900109175.1	915471	915471	type	True	81.9647	670	1540	95	below_threshold
Pseudomonas sagittaria	strain=JCM 18195	GCA_900115715.1	1135990	1135990	type	True	81.9453	682	1540	95	below_threshold
Azotobacter chroococcum	strain=DSM 2286	GCA_004339665.1	353	353	type	True	81.8741	687	1540	95	below_threshold
Azotobacter chroococcum subsp. isscasi	strain=P205	GCA_004327895.1	2528971	353	type	True	81.8549	695	1540	95	below_threshold
Pseudomonas indica	strain=JCM 21544	GCA_900100285.1	137658	137658	type	True	81.8175	862	1540	95	below_threshold
Pseudomonas indica	strain=NBRC 103045	GCA_002091635.1	137658	137658	type	True	81.8062	860	1540	95	below_threshold
Azotobacter chroococcum	strain=ATCC 9043	GCA_004327905.1	353	353	type	True	81.7836	693	1540	95	below_threshold
Azotobacter beijerinckii	strain=DSM 378	GCA_900110885.1	170623	170623	type	True	81.7193	658	1540	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:44,326] [INFO] DFAST Taxonomy check result was written to GCF_007109405.1_ASM710940v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:44,326] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:44,326] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:44,326] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4f51b7a6-1d0f-4f05-8bd9-98c5c1d44f99/dqc_reference/checkm_data
[2024-01-24 13:49:44,327] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:44,373] [INFO] Task started: CheckM
[2024-01-24 13:49:44,374] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007109405.1_ASM710940v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007109405.1_ASM710940v1_genomic.fna/checkm_input GCF_007109405.1_ASM710940v1_genomic.fna/checkm_result
[2024-01-24 13:50:29,992] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:29,994] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:30,012] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:30,012] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:30,013] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007109405.1_ASM710940v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:30,013] [INFO] Task started: Blastn
[2024-01-24 13:50:30,014] [INFO] Running command: blastn -query GCF_007109405.1_ASM710940v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f51b7a6-1d0f-4f05-8bd9-98c5c1d44f99/dqc_reference/reference_markers_gtdb.fasta -out GCF_007109405.1_ASM710940v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:31,987] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:31,991] [INFO] Selected 22 target genomes.
[2024-01-24 13:50:31,991] [INFO] Target genome list was writen to GCF_007109405.1_ASM710940v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:32,007] [INFO] Task started: fastANI
[2024-01-24 13:50:32,008] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc7a28fc-69ec-464f-b8de-23e6360d7cd6/GCF_007109405.1_ASM710940v1_genomic.fna.gz --refList GCF_007109405.1_ASM710940v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007109405.1_ASM710940v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:56,751] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:56,774] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:56,774] [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_007109405.1	s__VJOY01 sp007109405	100.0	1539	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__VJOY01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_012767755.2	s__Pseudomonas_F sp003234055	83.248	1043	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	96.89	96.11	0.89	0.88	3	-
GCF_018398425.1	s__Pseudomonas_E lalucatii	83.126	823	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.68	99.28	0.97	0.92	4	-
GCF_900187975.1	s__Pseudomonas delhiensis	83.068	985	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.078	98.79	97.59	0.94	0.89	3	-
GCF_009799925.1	s__Pseudomonas_E sp009799925	83.0048	847	1540	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_904061905.1	s__Pseudomonas_E carbonaria	82.9994	890	1540	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_902506505.1	s__Pseudomonas_E sp902506505	82.9829	831	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.45	95.45	0.88	0.88	2	-
GCF_900112375.1	s__Pseudomonas citronellolis	82.8778	987	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.078	97.44	97.08	0.86	0.82	26	-
GCF_002355475.1	s__Pseudomonas_F furukawaii	82.5907	889	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	99.26	98.53	0.90	0.84	3	-
GCF_000017205.1	s__Pseudomonas aeruginosa_A	82.443	950	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	99.07	98.78	0.93	0.80	42	-
GCF_900106975.1	s__Pseudomonas_O kuykendallii	82.2334	866	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_O	95.0	96.83	96.68	0.93	0.91	4	-
GCF_019097855.1	s__Pseudomonas_K sp019097855	82.1067	635	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001457615.1	s__Pseudomonas aeruginosa	82.072	954	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	99.12	97.38	0.94	0.84	5623	-
GCF_900115715.1	s__Pseudomonas_K sagittaria	81.9276	683	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339665.1	s__Azotobacter chroococcum	81.8173	693	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Azotobacter	95.0	97.27	96.18	0.89	0.83	10	-
GCF_002091635.1	s__Pseudomonas_M indica	81.8103	860	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_M	95.0	99.16	98.73	0.94	0.91	4	-
GCF_000425625.1	s__Pseudomonas_N azotifigens	81.8086	772	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_N	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002890915.1	s__Pseudomonas_A stutzeri_AF	81.7561	747	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.35	98.08	0.91	0.89	3	-
GCF_900110885.1	s__Azotobacter beijerinckii	81.7131	658	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Azotobacter	95.0	97.34	96.47	0.86	0.85	5	-
GCF_009363155.1	s__Azotobacter salinestris	81.4765	678	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Azotobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015070855.1	s__Pseudomonas_A lopnurensis	81.3657	749	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.76	98.41	0.83	0.83	4	-
GCF_000380335.1	s__Azotobacter vinelandii	81.1172	673	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Azotobacter	95.0	99.84	99.43	0.98	0.95	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:56,776] [INFO] GTDB search result was written to GCF_007109405.1_ASM710940v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:56,777] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:56,783] [INFO] DFAST_QC result json was written to GCF_007109405.1_ASM710940v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:56,783] [INFO] DFAST_QC completed!
[2024-01-24 13:50:56,783] [INFO] Total running time: 0h1m57s