[2024-01-24 13:41:26,589] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:26,592] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:26,592] [INFO] DQC Reference Directory: /var/lib/cwl/stgc244f197-57ec-4d7e-90de-c1ac5b1c3238/dqc_reference
[2024-01-24 13:41:28,084] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:28,085] [INFO] Task started: Prodigal
[2024-01-24 13:41:28,086] [INFO] Running command: gunzip -c /var/lib/cwl/stg162e97ee-973e-4393-9f09-355109212a2a/GCF_900459405.1_41965_B01_genomic.fna.gz | prodigal -d GCF_900459405.1_41965_B01_genomic.fna/cds.fna -a GCF_900459405.1_41965_B01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:34,615] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:34,615] [INFO] Task started: HMMsearch
[2024-01-24 13:41:34,615] [INFO] Running command: hmmsearch --tblout GCF_900459405.1_41965_B01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc244f197-57ec-4d7e-90de-c1ac5b1c3238/dqc_reference/reference_markers.hmm GCF_900459405.1_41965_B01_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:34,894] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:34,895] [INFO] Found 6/6 markers.
[2024-01-24 13:41:34,923] [INFO] Query marker FASTA was written to GCF_900459405.1_41965_B01_genomic.fna/markers.fasta
[2024-01-24 13:41:34,924] [INFO] Task started: Blastn
[2024-01-24 13:41:34,924] [INFO] Running command: blastn -query GCF_900459405.1_41965_B01_genomic.fna/markers.fasta -db /var/lib/cwl/stgc244f197-57ec-4d7e-90de-c1ac5b1c3238/dqc_reference/reference_markers.fasta -out GCF_900459405.1_41965_B01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:35,561] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:35,601] [INFO] Selected 29 target genomes.
[2024-01-24 13:41:35,602] [INFO] Target genome list was writen to GCF_900459405.1_41965_B01_genomic.fna/target_genomes.txt
[2024-01-24 13:41:35,614] [INFO] Task started: fastANI
[2024-01-24 13:41:35,615] [INFO] Running command: fastANI --query /var/lib/cwl/stg162e97ee-973e-4393-9f09-355109212a2a/GCF_900459405.1_41965_B01_genomic.fna.gz --refList GCF_900459405.1_41965_B01_genomic.fna/target_genomes.txt --output GCF_900459405.1_41965_B01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:47,429] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:47,430] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc244f197-57ec-4d7e-90de-c1ac5b1c3238/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:47,430] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc244f197-57ec-4d7e-90de-c1ac5b1c3238/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:47,456] [INFO] Found 29 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:47,456] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:47,457] [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
Streptococcus hyointestinalis	strain=NCTC12224	GCA_900459405.1	1337	1337	type	True	100.0	846	848	95	conclusive
Streptococcus parasuis	strain=SUT-286	GCA_021654455.1	1501662	1501662	suspected-type	True	82.1201	85	848	95	below_threshold
Streptococcus pyogenes	strain=PartK-Spyogenes-RM8376	GCA_022869605.1	1314	1314	type	True	81.3416	86	848	95	below_threshold
Streptococcus pyogenes	strain=CCUG 4207	GCA_004028355.1	1314	1314	type	True	81.325	85	848	95	below_threshold
Streptococcus cristatus	strain=ATCC 51100	GCA_000222765.2	45634	45634	type	True	80.7555	102	848	95	below_threshold
Streptococcus porci	strain=DSM 23759	GCA_000423765.1	502567	502567	type	True	80.7518	112	848	95	below_threshold
Streptococcus canis	strain=NCTC12191	GCA_900636575.1	1329	1329	type	True	80.7158	98	848	95	below_threshold
Streptococcus cristatus	strain=NCTC12479	GCA_900475445.1	45634	45634	type	True	80.5818	101	848	95	below_threshold
Streptococcus constellatus subsp. constellatus	strain=CCUG 24889	GCA_023167545.1	184246	76860	type	True	80.3069	89	848	95	below_threshold
Streptococcus toyakuensis	strain=TP1632	GCA_024346585.1	2819619	2819619	type	True	80.0397	114	848	95	below_threshold
Streptococcus equinus	strain=NCTC12969	GCA_900459295.1	1335	1335	type	True	79.8724	125	848	95	below_threshold
Streptococcus sobrinus	strain=SL1	GCA_003172995.1	1310	1310	type	True	79.6614	90	848	95	below_threshold
Streptococcus cristatus	strain=ATCC 51100	GCA_000187855.1	45634	45634	type	True	79.6217	99	848	95	below_threshold
Streptococcus sobrinus	strain=NCTC12279	GCA_900475395.1	1310	1310	type	True	79.6151	92	848	95	below_threshold
Streptococcus pyogenes	strain=DSM 20565	GCA_000421785.1	1314	1314	type	True	79.5715	79	848	95	below_threshold
Streptococcus downii	strain=CECT 9732	GCA_004353325.1	1968889	1968889	type	True	79.3335	103	848	95	below_threshold
Streptococcus hillyeri	strain=28462	GCA_003686955.1	2282420	2282420	type	True	79.2824	107	848	95	below_threshold
Streptococcus vicugnae	strain=SL1232	GCA_016461705.1	2740579	2740579	type	True	79.1596	111	848	95	below_threshold
Streptococcus acidominimus	strain=CCUG 27296	GCA_001921825.1	1326	1326	type	True	79.035	78	848	95	below_threshold
Streptococcus loxodontisalivarius	strain=DSM 27382	GCA_016908645.1	1349415	1349415	type	True	78.9739	142	848	95	below_threshold
Streptococcus thoraltensis	strain=DSM 12221	GCA_000380145.1	55085	55085	type	True	78.962	107	848	95	below_threshold
Streptococcus vulneris	strain=DM3B3	GCA_019218685.1	2853160	2853160	type	True	78.7924	95	848	95	below_threshold
Streptococcus equinus	strain=ATCC 9812	GCA_000187265.1	1335	1335	type	True	78.7786	113	848	95	below_threshold
Streptococcus oralis	strain=ATCC 35037	GCA_000164095.1	1303	1303	type	True	78.6665	86	848	95	below_threshold
Streptococcus oralis	strain=CCUG 13229	GCA_002014885.1	1303	1303	type	True	78.6401	88	848	95	below_threshold
Streptococcus pharyngis	strain=CCUG 66496	GCA_007859195.1	1562651	1562651	type	True	78.4962	81	848	95	below_threshold
Streptococcus oralis	strain=CCUG 24891	GCA_001639375.1	1303	1303	type	True	78.3803	89	848	95	below_threshold
Streptococcus sobrinus	strain=ATCC 33478	GCA_000439045.1	1310	1310	type	True	78.2496	84	848	95	below_threshold
Streptococcus sobrinus	strain=DSM 20742	GCA_000686605.1	1310	1310	type	True	78.1718	84	848	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:47,461] [INFO] DFAST Taxonomy check result was written to GCF_900459405.1_41965_B01_genomic.fna/tc_result.tsv
[2024-01-24 13:41:47,462] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:47,462] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:47,463] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc244f197-57ec-4d7e-90de-c1ac5b1c3238/dqc_reference/checkm_data
[2024-01-24 13:41:47,465] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:47,498] [INFO] Task started: CheckM
[2024-01-24 13:41:47,498] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900459405.1_41965_B01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900459405.1_41965_B01_genomic.fna/checkm_input GCF_900459405.1_41965_B01_genomic.fna/checkm_result
[2024-01-24 13:42:11,933] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:11,934] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:11,954] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:11,954] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:11,955] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900459405.1_41965_B01_genomic.fna/markers.fasta)
[2024-01-24 13:42:11,955] [INFO] Task started: Blastn
[2024-01-24 13:42:11,955] [INFO] Running command: blastn -query GCF_900459405.1_41965_B01_genomic.fna/markers.fasta -db /var/lib/cwl/stgc244f197-57ec-4d7e-90de-c1ac5b1c3238/dqc_reference/reference_markers_gtdb.fasta -out GCF_900459405.1_41965_B01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:12,835] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:12,839] [INFO] Selected 23 target genomes.
[2024-01-24 13:42:12,840] [INFO] Target genome list was writen to GCF_900459405.1_41965_B01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:12,858] [INFO] Task started: fastANI
[2024-01-24 13:42:12,859] [INFO] Running command: fastANI --query /var/lib/cwl/stg162e97ee-973e-4393-9f09-355109212a2a/GCF_900459405.1_41965_B01_genomic.fna.gz --refList GCF_900459405.1_41965_B01_genomic.fna/target_genomes_gtdb.txt --output GCF_900459405.1_41965_B01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:22,793] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:22,820] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:22,821] [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_900459405.1	s__Streptococcus hyointestinalis	100.0	846	848	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011039275.1	s__Streptococcus hyointestinalis_A	93.6236	528	848	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423765.1	s__Streptococcus porci	80.7847	113	848	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000222765.1	s__Streptococcus cristatus	80.696	103	848	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.39	95.04	0.92	0.87	17	-
GCF_900636575.1	s__Streptococcus canis	80.6218	99	848	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.95	97.68	0.91	0.86	20	-
GCF_000253155.1	s__Streptococcus oralis_L	80.5158	104	848	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.38	95.38	0.91	0.91	2	-
GCF_009738225.1	s__Streptococcus sp001556435	80.3121	119	848	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.11	95.45	0.91	0.84	79	-
GCF_900636475.1	s__Streptococcus anginosus	79.7454	85	848	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	96.16	95.41	0.84	0.78	79	-
GCA_905221455.1	s__Streptococcus sp905221455	79.7069	94	848	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001697145.1	s__Streptococcus anginosus_C	79.6254	85	848	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.71	95.87	0.90	0.80	41	-
GCF_003686955.1	s__Streptococcus sp003686955	79.2734	107	848	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001171885.1	s__Streptococcus pneumoniae_A	79.2259	109	848	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016461705.1	s__Streptococcus vicugnae	79.1274	113	848	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	98.43	98.30	0.94	0.90	4	-
GCA_905221215.1	s__Streptococcus sp905221215	78.999	92	848	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.24	95.24	0.89	0.89	2	-
GCF_000380145.1	s__Streptococcus thoraltensis	78.962	107	848	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003942675.1	s__Streptococcus oralis_BC	78.7843	86	848	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	95.25	95.12	0.91	0.89	7	-
GCF_000187265.1	s__Streptococcus equinus	78.7774	113	848	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	97.03	95.86	0.90	0.87	42	-
GCA_905221545.1	s__Streptococcus sp905221545	78.7141	107	848	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001578795.1	s__Streptococcus gordonii_A	78.6281	89	848	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859195.1	s__Streptococcus pharyngis	78.5011	82	848	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902167705.1	s__Streptococcus constellatus_A	78.5005	80	848	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003942965.1	s__Streptococcus mitis_BH	78.4482	103	848	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015594605.1	s__Streptococcus sp015594605	78.3919	162	848	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:22,822] [INFO] GTDB search result was written to GCF_900459405.1_41965_B01_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:22,823] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:22,828] [INFO] DFAST_QC result json was written to GCF_900459405.1_41965_B01_genomic.fna/dqc_result.json
[2024-01-24 13:42:22,828] [INFO] DFAST_QC completed!
[2024-01-24 13:42:22,828] [INFO] Total running time: 0h0m56s