[2024-01-24 13:13:46,774] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:46,776] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:46,776] [INFO] DQC Reference Directory: /var/lib/cwl/stg9c01e206-cb4c-4747-ae7f-b3a8fd2c836f/dqc_reference
[2024-01-24 13:13:48,049] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:48,050] [INFO] Task started: Prodigal
[2024-01-24 13:13:48,051] [INFO] Running command: gunzip -c /var/lib/cwl/stg5019bfb7-66ad-417d-9c35-0be3a2c57e15/GCF_013306565.1_ASM1330656v1_genomic.fna.gz | prodigal -d GCF_013306565.1_ASM1330656v1_genomic.fna/cds.fna -a GCF_013306565.1_ASM1330656v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:59,093] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:59,094] [INFO] Task started: HMMsearch
[2024-01-24 13:13:59,094] [INFO] Running command: hmmsearch --tblout GCF_013306565.1_ASM1330656v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9c01e206-cb4c-4747-ae7f-b3a8fd2c836f/dqc_reference/reference_markers.hmm GCF_013306565.1_ASM1330656v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:59,351] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:59,353] [INFO] Found 6/6 markers.
[2024-01-24 13:13:59,391] [INFO] Query marker FASTA was written to GCF_013306565.1_ASM1330656v1_genomic.fna/markers.fasta
[2024-01-24 13:13:59,391] [INFO] Task started: Blastn
[2024-01-24 13:13:59,391] [INFO] Running command: blastn -query GCF_013306565.1_ASM1330656v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c01e206-cb4c-4747-ae7f-b3a8fd2c836f/dqc_reference/reference_markers.fasta -out GCF_013306565.1_ASM1330656v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:00,313] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:00,317] [INFO] Selected 17 target genomes.
[2024-01-24 13:14:00,318] [INFO] Target genome list was writen to GCF_013306565.1_ASM1330656v1_genomic.fna/target_genomes.txt
[2024-01-24 13:14:00,345] [INFO] Task started: fastANI
[2024-01-24 13:14:00,345] [INFO] Running command: fastANI --query /var/lib/cwl/stg5019bfb7-66ad-417d-9c35-0be3a2c57e15/GCF_013306565.1_ASM1330656v1_genomic.fna.gz --refList GCF_013306565.1_ASM1330656v1_genomic.fna/target_genomes.txt --output GCF_013306565.1_ASM1330656v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:14:13,647] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:13,648] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9c01e206-cb4c-4747-ae7f-b3a8fd2c836f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:14:13,648] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9c01e206-cb4c-4747-ae7f-b3a8fd2c836f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:14:13,661] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:14:13,661] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:14:13,661] [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
Hyphomicrobium sulfonivorans	strain=S1	GCA_013306565.1	121290	121290	type	True	100.0	1176	1177	95	conclusive
Hyphomicrobium sulfonivorans	strain=S1	GCA_016125985.1	121290	121290	type	True	99.9965	1172	1177	95	conclusive
Hyphomicrobium album	strain=XQ2	GCA_009708035.1	2665159	2665159	type	True	79.2687	510	1177	95	below_threshold
Hyphomicrobium nitrativorans	strain=NL23	GCA_000503895.1	1427356	1427356	type	True	77.7969	257	1177	95	below_threshold
Hyphomicrobium zavarzinii	strain=ZV-622	GCA_000383415.1	48292	48292	type	True	77.7556	273	1177	95	below_threshold
Hyphomicrobium denitrificans	strain=ATCC 51888	GCA_000143145.1	53399	53399	type	True	77.5656	230	1177	95	below_threshold
Hyphomicrobium facile	strain=DSM 1565	GCA_900116175.1	51670	51670	type	True	77.5396	186	1177	95	below_threshold
Pyruvatibacter mobilis	strain=GYP-11	GCA_009910475.1	1712261	1712261	type	True	77.0397	86	1177	95	below_threshold
Aestuariivirga litoralis	strain=KCTC 52945	GCA_003234965.1	2650924	2650924	type	True	76.9672	114	1177	95	below_threshold
Roseibium litorale	strain=4C16A	GCA_014842915.1	2803841	2803841	type	True	76.6985	75	1177	95	below_threshold
Rhodoplanes piscinae	strain=DSM 19946	GCA_003258855.1	444923	444923	type	True	76.6223	146	1177	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	76.5082	109	1177	95	below_threshold
Stappia taiwanensis	strain=CCM 7757	GCA_014635285.1	992267	992267	type	True	76.4698	106	1177	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	76.452	117	1177	95	below_threshold
Shinella daejeonensis	strain=JCM 16236	GCA_024281235.1	659017	659017	type	True	76.4434	101	1177	95	below_threshold
Rhodobacter calidifons	strain=M37P	GCA_011174775.1	2715277	2715277	type	True	76.1838	55	1177	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	76.114	121	1177	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:14:13,663] [INFO] DFAST Taxonomy check result was written to GCF_013306565.1_ASM1330656v1_genomic.fna/tc_result.tsv
[2024-01-24 13:14:13,664] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:14:13,664] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:14:13,664] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9c01e206-cb4c-4747-ae7f-b3a8fd2c836f/dqc_reference/checkm_data
[2024-01-24 13:14:13,665] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:14:13,708] [INFO] Task started: CheckM
[2024-01-24 13:14:13,708] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013306565.1_ASM1330656v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013306565.1_ASM1330656v1_genomic.fna/checkm_input GCF_013306565.1_ASM1330656v1_genomic.fna/checkm_result
[2024-01-24 13:14:50,090] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:50,091] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:50,111] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:50,112] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:50,112] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013306565.1_ASM1330656v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:50,113] [INFO] Task started: Blastn
[2024-01-24 13:14:50,113] [INFO] Running command: blastn -query GCF_013306565.1_ASM1330656v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c01e206-cb4c-4747-ae7f-b3a8fd2c836f/dqc_reference/reference_markers_gtdb.fasta -out GCF_013306565.1_ASM1330656v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:51,889] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:51,893] [INFO] Selected 13 target genomes.
[2024-01-24 13:14:51,893] [INFO] Target genome list was writen to GCF_013306565.1_ASM1330656v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:51,904] [INFO] Task started: fastANI
[2024-01-24 13:14:51,904] [INFO] Running command: fastANI --query /var/lib/cwl/stg5019bfb7-66ad-417d-9c35-0be3a2c57e15/GCF_013306565.1_ASM1330656v1_genomic.fna.gz --refList GCF_013306565.1_ASM1330656v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013306565.1_ASM1330656v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:15:02,856] [INFO] Task succeeded: fastANI
[2024-01-24 13:15:02,867] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:15:02,867] [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_013306565.1	s__Hyphomicrobium_A sulfonivorans	100.0	1175	1177	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium_A	95.0	98.55	97.10	0.95	0.91	3	conclusive
GCF_009708035.1	s__Hyphomicrobium_A sp009708035	79.2733	509	1177	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900117445.1	s__Hyphomicrobium_A sp900117445	79.1156	503	1177	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009026145.1	s__Hyphomicrobium_A sp009026145	78.8851	537	1177	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000383415.1	s__Hyphomicrobium zavarzinii	77.7556	273	1177	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	98.69	98.69	0.95	0.95	2	-
GCA_902826555.1	s__Hyphomicrobium sp902826555	77.6426	231	1177	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116175.1	s__Hyphomicrobium facile	77.5231	187	1177	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000253295.1	s__Hyphomicrobium sp000253295	77.4443	198	1177	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	99.46	99.46	0.96	0.96	2	-
GCA_017304275.1	s__Hyphomicrobium sp017304275	77.4398	181	1177	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003963125.1	s__AWTP1-13 sp003963125	77.4211	200	1177	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__AWTP1-13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003242645.1	s__ZC4RG25 sp003242645	76.6358	111	1177	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__ZC4RG25	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009720755.1	s__Rhodoplanes serenus	76.5631	168	1177	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	97.72	97.48	0.91	0.88	4	-
GCA_019240125.1	s__AP-15 sp019240125	75.4661	51	1177	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__AP-15	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:15:02,869] [INFO] GTDB search result was written to GCF_013306565.1_ASM1330656v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:15:02,870] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:15:02,873] [INFO] DFAST_QC result json was written to GCF_013306565.1_ASM1330656v1_genomic.fna/dqc_result.json
[2024-01-24 13:15:02,874] [INFO] DFAST_QC completed!
[2024-01-24 13:15:02,874] [INFO] Total running time: 0h1m16s