[2023-06-19 05:25:11,022] [INFO] DFAST_QC pipeline started.
[2023-06-19 05:25:11,026] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 05:25:11,026] [INFO] DQC Reference Directory: /var/lib/cwl/stg587e7d2f-f9d7-4bbd-b574-0e77e34d0e65/dqc_reference
[2023-06-19 05:25:12,264] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 05:25:12,265] [INFO] Task started: Prodigal
[2023-06-19 05:25:12,266] [INFO] Running command: gunzip -c /var/lib/cwl/stg25ac5ab1-d40b-46f5-9320-5aaa44db2a4a/GCA_018369315.1_ASM1836931v1_genomic.fna.gz | prodigal -d GCA_018369315.1_ASM1836931v1_genomic.fna/cds.fna -a GCA_018369315.1_ASM1836931v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 05:25:27,281] [INFO] Task succeeded: Prodigal
[2023-06-19 05:25:27,281] [INFO] Task started: HMMsearch
[2023-06-19 05:25:27,282] [INFO] Running command: hmmsearch --tblout GCA_018369315.1_ASM1836931v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg587e7d2f-f9d7-4bbd-b574-0e77e34d0e65/dqc_reference/reference_markers.hmm GCA_018369315.1_ASM1836931v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 05:25:27,574] [INFO] Task succeeded: HMMsearch
[2023-06-19 05:25:27,576] [INFO] Found 6/6 markers.
[2023-06-19 05:25:27,608] [INFO] Query marker FASTA was written to GCA_018369315.1_ASM1836931v1_genomic.fna/markers.fasta
[2023-06-19 05:25:27,609] [INFO] Task started: Blastn
[2023-06-19 05:25:27,609] [INFO] Running command: blastn -query GCA_018369315.1_ASM1836931v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg587e7d2f-f9d7-4bbd-b574-0e77e34d0e65/dqc_reference/reference_markers.fasta -out GCA_018369315.1_ASM1836931v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 05:25:28,285] [INFO] Task succeeded: Blastn
[2023-06-19 05:25:28,293] [INFO] Selected 16 target genomes.
[2023-06-19 05:25:28,294] [INFO] Target genome list was writen to GCA_018369315.1_ASM1836931v1_genomic.fna/target_genomes.txt
[2023-06-19 05:25:28,297] [INFO] Task started: fastANI
[2023-06-19 05:25:28,297] [INFO] Running command: fastANI --query /var/lib/cwl/stg25ac5ab1-d40b-46f5-9320-5aaa44db2a4a/GCA_018369315.1_ASM1836931v1_genomic.fna.gz --refList GCA_018369315.1_ASM1836931v1_genomic.fna/target_genomes.txt --output GCA_018369315.1_ASM1836931v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 05:25:38,330] [INFO] Task succeeded: fastANI
[2023-06-19 05:25:38,331] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg587e7d2f-f9d7-4bbd-b574-0e77e34d0e65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 05:25:38,331] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg587e7d2f-f9d7-4bbd-b574-0e77e34d0e65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 05:25:38,347] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2023-06-19 05:25:38,347] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-19 05:25:38,347] [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
Alistipes communis	strain=5CBH24	GCA_006542665.1	2585118	2585118	type	True	98.908	843	910	95	conclusive
Alistipes dispar	strain=5CPEGH6	GCA_006542685.1	2585119	2585119	type	True	81.8236	417	910	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_000210575.1	328814	328814	suspected-type	True	80.2205	403	910	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_025145845.1	328814	328814	suspected-type	True	80.2072	394	910	95	below_threshold
Alistipes provencensis	strain=Marseille-P2431	GCA_900083545.1	1816676	1816676	type	True	80.166	394	910	95	below_threshold
Alistipes senegalensis	strain=FDAARGOS_1578	GCA_020735725.1	1288121	1288121	type	True	80.1199	410	910	95	below_threshold
Alistipes senegalensis	strain=JC50	GCA_025145645.1	1288121	1288121	type	True	80.0763	414	910	95	below_threshold
Alistipes timonensis	strain=DSM 25383	GCA_900107675.1	1465754	1465754	type	True	80.0653	371	910	95	below_threshold
Alistipes senegalensis	strain=JC50	GCA_000312145.1	1288121	1288121	type	True	80.0267	412	910	95	below_threshold
Alistipes finegoldii	strain=DSM 17242	GCA_000265365.1	214856	214856	type	True	79.7429	389	910	95	below_threshold
Alistipes megaguti	strain=Marseille-P5997	GCA_900604385.1	2364787	2364787	type	True	79.6951	346	910	95	below_threshold
Alistipes montrealensis	strain=kh20	GCA_018362775.1	2834113	2834113	type	True	79.3596	379	910	95	below_threshold
Alistipes onderdonkii	strain=DSM 19147	GCA_000374505.1	328813	328813	type	True	79.3588	392	910	95	below_threshold
Alistipes onderdonkii	strain=DSM 19147	GCA_025145285.1	328813	328813	type	True	79.2298	406	910	95	below_threshold
Alistipes onderdonkii subsp. vulgaris	strain=3BBH6	GCA_006542645.1	2585117	328813	type	True	79.1679	385	910	95	below_threshold
Alistipes ihumii	strain=AP11	GCA_025144665.1	1470347	1470347	type	True	77.4304	140	910	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 05:25:38,350] [INFO] DFAST Taxonomy check result was written to GCA_018369315.1_ASM1836931v1_genomic.fna/tc_result.tsv
[2023-06-19 05:25:38,351] [INFO] ===== Taxonomy check completed =====
[2023-06-19 05:25:38,351] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 05:25:38,351] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg587e7d2f-f9d7-4bbd-b574-0e77e34d0e65/dqc_reference/checkm_data
[2023-06-19 05:25:38,353] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 05:25:38,386] [INFO] Task started: CheckM
[2023-06-19 05:25:38,386] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018369315.1_ASM1836931v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018369315.1_ASM1836931v1_genomic.fna/checkm_input GCA_018369315.1_ASM1836931v1_genomic.fna/checkm_result
[2023-06-19 05:26:21,591] [INFO] Task succeeded: CheckM
[2023-06-19 05:26:21,592] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 05:26:21,621] [INFO] ===== Completeness check finished =====
[2023-06-19 05:26:21,621] [INFO] ===== Start GTDB Search =====
[2023-06-19 05:26:21,622] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018369315.1_ASM1836931v1_genomic.fna/markers.fasta)
[2023-06-19 05:26:21,622] [INFO] Task started: Blastn
[2023-06-19 05:26:21,622] [INFO] Running command: blastn -query GCA_018369315.1_ASM1836931v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg587e7d2f-f9d7-4bbd-b574-0e77e34d0e65/dqc_reference/reference_markers_gtdb.fasta -out GCA_018369315.1_ASM1836931v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 05:26:22,595] [INFO] Task succeeded: Blastn
[2023-06-19 05:26:22,603] [INFO] Selected 14 target genomes.
[2023-06-19 05:26:22,604] [INFO] Target genome list was writen to GCA_018369315.1_ASM1836931v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 05:26:22,613] [INFO] Task started: fastANI
[2023-06-19 05:26:22,613] [INFO] Running command: fastANI --query /var/lib/cwl/stg25ac5ab1-d40b-46f5-9320-5aaa44db2a4a/GCA_018369315.1_ASM1836931v1_genomic.fna.gz --refList GCA_018369315.1_ASM1836931v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018369315.1_ASM1836931v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 05:26:30,881] [INFO] Task succeeded: fastANI
[2023-06-19 05:26:30,896] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 05:26:30,896] [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_006542665.1	s__Alistipes communis	98.908	843	910	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.74	98.62	0.92	0.87	10	conclusive
GCA_900550375.1	s__Alistipes sp900550375	87.5692	556	910	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	100.00	100.00	0.99	0.99	2	-
GCA_900552955.1	s__Alistipes sp900552955	86.8927	422	910	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905214725.1	s__Alistipes sp905214725	86.3453	604	910	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006542685.1	s__Alistipes dispar	81.8236	417	910	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	99.07	98.96	0.94	0.89	7	-
GCF_900021155.1	s__Alistipes excrementavium	80.9741	361	910	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	99.37	98.83	0.93	0.90	7	-
GCA_902362705.1	s__Alistipes sp002358415	80.3413	341	910	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	99.62	98.83	0.97	0.92	7	-
GCA_900544265.1	s__Alistipes merdavium	80.3246	338	910	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.60	98.07	0.91	0.88	5	-
GCA_900541585.1	s__Alistipes sp900541585	79.942	379	910	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.86	98.76	0.92	0.91	4	-
GCF_002161445.1	s__Alistipes cottocaccae	79.885	341	910	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.26	98.26	0.94	0.94	2	-
GCF_000265365.1	s__Alistipes finegoldii	79.7429	389	910	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.50	97.54	0.87	0.79	15	-
GCF_900290115.1	s__Alistipes excrementigallinarum	79.5296	349	910	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.90	98.75	0.93	0.91	6	-
GCA_019118605.1	s__Alistipes faecavium	79.4783	318	910	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019113885.1	s__Alistipes intestinipullorum	78.7203	265	910	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 05:26:30,899] [INFO] GTDB search result was written to GCA_018369315.1_ASM1836931v1_genomic.fna/result_gtdb.tsv
[2023-06-19 05:26:30,899] [INFO] ===== GTDB Search completed =====
[2023-06-19 05:26:30,904] [INFO] DFAST_QC result json was written to GCA_018369315.1_ASM1836931v1_genomic.fna/dqc_result.json
[2023-06-19 05:26:30,904] [INFO] DFAST_QC completed!
[2023-06-19 05:26:30,904] [INFO] Total running time: 0h1m20s