[2023-06-28 14:52:26,072] [INFO] DFAST_QC pipeline started.
[2023-06-28 14:52:26,074] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 14:52:26,074] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc971754-6acc-45ec-bc84-25c7823c6251/dqc_reference
[2023-06-28 14:52:27,263] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 14:52:27,263] [INFO] Task started: Prodigal
[2023-06-28 14:52:27,264] [INFO] Running command: gunzip -c /var/lib/cwl/stge50d4811-28ed-4070-b0bc-f0afa42aaf47/GCA_020853095.1_ASM2085309v1_genomic.fna.gz | prodigal -d GCA_020853095.1_ASM2085309v1_genomic.fna/cds.fna -a GCA_020853095.1_ASM2085309v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 14:52:37,527] [INFO] Task succeeded: Prodigal
[2023-06-28 14:52:37,527] [INFO] Task started: HMMsearch
[2023-06-28 14:52:37,528] [INFO] Running command: hmmsearch --tblout GCA_020853095.1_ASM2085309v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc971754-6acc-45ec-bc84-25c7823c6251/dqc_reference/reference_markers.hmm GCA_020853095.1_ASM2085309v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 14:52:37,754] [INFO] Task succeeded: HMMsearch
[2023-06-28 14:52:37,755] [INFO] Found 6/6 markers.
[2023-06-28 14:52:37,785] [INFO] Query marker FASTA was written to GCA_020853095.1_ASM2085309v1_genomic.fna/markers.fasta
[2023-06-28 14:52:37,785] [INFO] Task started: Blastn
[2023-06-28 14:52:37,785] [INFO] Running command: blastn -query GCA_020853095.1_ASM2085309v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc971754-6acc-45ec-bc84-25c7823c6251/dqc_reference/reference_markers.fasta -out GCA_020853095.1_ASM2085309v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 14:52:38,333] [INFO] Task succeeded: Blastn
[2023-06-28 14:52:38,336] [INFO] Selected 22 target genomes.
[2023-06-28 14:52:38,336] [INFO] Target genome list was writen to GCA_020853095.1_ASM2085309v1_genomic.fna/target_genomes.txt
[2023-06-28 14:52:38,338] [INFO] Task started: fastANI
[2023-06-28 14:52:38,338] [INFO] Running command: fastANI --query /var/lib/cwl/stge50d4811-28ed-4070-b0bc-f0afa42aaf47/GCA_020853095.1_ASM2085309v1_genomic.fna.gz --refList GCA_020853095.1_ASM2085309v1_genomic.fna/target_genomes.txt --output GCA_020853095.1_ASM2085309v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 14:52:57,445] [INFO] Task succeeded: fastANI
[2023-06-28 14:52:57,446] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc971754-6acc-45ec-bc84-25c7823c6251/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 14:52:57,446] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc971754-6acc-45ec-bc84-25c7823c6251/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 14:52:57,451] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 14:52:57,451] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 14:52:57,451] [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
Humisphaera borealis	strain=M1803	GCA_015169395.1	2807512	2807512	type	True	76.4925	116	1169	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	75.2588	54	1169	95	below_threshold
Posidoniimonas polymericola	strain=Pla123a	GCA_007859935.1	2528002	2528002	type	True	75.2365	50	1169	95	below_threshold
Tautonia plasticadhaerens	strain=ElP	GCA_007752535.1	2527974	2527974	type	True	74.842	59	1169	95	below_threshold
Azospirillum cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	74.7436	66	1169	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 14:52:57,453] [INFO] DFAST Taxonomy check result was written to GCA_020853095.1_ASM2085309v1_genomic.fna/tc_result.tsv
[2023-06-28 14:52:57,453] [INFO] ===== Taxonomy check completed =====
[2023-06-28 14:52:57,453] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 14:52:57,454] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc971754-6acc-45ec-bc84-25c7823c6251/dqc_reference/checkm_data
[2023-06-28 14:52:57,454] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 14:52:57,492] [INFO] Task started: CheckM
[2023-06-28 14:52:57,492] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020853095.1_ASM2085309v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020853095.1_ASM2085309v1_genomic.fna/checkm_input GCA_020853095.1_ASM2085309v1_genomic.fna/checkm_result
[2023-06-28 14:53:33,457] [INFO] Task succeeded: CheckM
[2023-06-28 14:53:33,458] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 14:53:33,473] [INFO] ===== Completeness check finished =====
[2023-06-28 14:53:33,473] [INFO] ===== Start GTDB Search =====
[2023-06-28 14:53:33,473] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020853095.1_ASM2085309v1_genomic.fna/markers.fasta)
[2023-06-28 14:53:33,474] [INFO] Task started: Blastn
[2023-06-28 14:53:33,474] [INFO] Running command: blastn -query GCA_020853095.1_ASM2085309v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc971754-6acc-45ec-bc84-25c7823c6251/dqc_reference/reference_markers_gtdb.fasta -out GCA_020853095.1_ASM2085309v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 14:53:34,208] [INFO] Task succeeded: Blastn
[2023-06-28 14:53:34,211] [INFO] Selected 18 target genomes.
[2023-06-28 14:53:34,211] [INFO] Target genome list was writen to GCA_020853095.1_ASM2085309v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 14:53:34,266] [INFO] Task started: fastANI
[2023-06-28 14:53:34,266] [INFO] Running command: fastANI --query /var/lib/cwl/stge50d4811-28ed-4070-b0bc-f0afa42aaf47/GCA_020853095.1_ASM2085309v1_genomic.fna.gz --refList GCA_020853095.1_ASM2085309v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020853095.1_ASM2085309v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 14:53:46,822] [INFO] Task succeeded: fastANI
[2023-06-28 14:53:46,828] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 14:53:46,828] [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
GCA_002311745.1	s__UBA1161 sp002311745	77.0117	144	1169	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Tepidisphaerales;f__Tepidisphaeraceae;g__UBA1161	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011367345.1	s__DSYW01 sp011367345	76.7782	190	1169	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Tepidisphaerales;f__Tepidisphaeraceae;g__DSYW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015169395.1	s__Humisphaera borealis	76.4925	116	1169	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Tepidisphaerales;f__Tepidisphaeraceae;g__Humisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003153655.1	s__PALSA-1353 sp003153655	76.0954	93	1169	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Tepidisphaerales;f__Tepidisphaeraceae;g__PALSA-1353	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014379105.1	s__JACMML01 sp014379105	75.9833	74	1169	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Tepidisphaerales;f__Tepidisphaeraceae;g__JACMML01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011358525.1	s__DTNO01 sp011358525	75.7933	59	1169	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Tepidisphaerales;f__Tepidisphaeraceae;g__DTNO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903871935.1	s__CAIQIQ01 sp903871935	75.757	95	1169	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Tepidisphaerales;f__Tepidisphaeraceae;g__CAIQIQ01	95.0	99.93	99.88	0.97	0.95	13	-
GCA_014380825.1	s__JACMJD01 sp014380825	75.6989	76	1169	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Tepidisphaerales;f__Tepidisphaeraceae;g__JACMJD01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 14:53:46,854] [INFO] GTDB search result was written to GCA_020853095.1_ASM2085309v1_genomic.fna/result_gtdb.tsv
[2023-06-28 14:53:46,855] [INFO] ===== GTDB Search completed =====
[2023-06-28 14:53:46,857] [INFO] DFAST_QC result json was written to GCA_020853095.1_ASM2085309v1_genomic.fna/dqc_result.json
[2023-06-28 14:53:46,857] [INFO] DFAST_QC completed!
[2023-06-28 14:53:46,857] [INFO] Total running time: 0h1m21s