[2023-06-13 14:27:34,974] [INFO] DFAST_QC pipeline started.
[2023-06-13 14:27:34,976] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 14:27:34,976] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ecb4e96-ffba-4e75-b33b-3fc50d314a51/dqc_reference
[2023-06-13 14:27:37,927] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 14:27:37,928] [INFO] Task started: Prodigal
[2023-06-13 14:27:37,928] [INFO] Running command: gunzip -c /var/lib/cwl/stgb2de6ee4-5604-422d-b4e0-2ccad435a5d8/GCA_022744865.1_ASM2274486v1_genomic.fna.gz | prodigal -d GCA_022744865.1_ASM2274486v1_genomic.fna/cds.fna -a GCA_022744865.1_ASM2274486v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 14:27:54,464] [INFO] Task succeeded: Prodigal
[2023-06-13 14:27:54,465] [INFO] Task started: HMMsearch
[2023-06-13 14:27:54,465] [INFO] Running command: hmmsearch --tblout GCA_022744865.1_ASM2274486v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ecb4e96-ffba-4e75-b33b-3fc50d314a51/dqc_reference/reference_markers.hmm GCA_022744865.1_ASM2274486v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 14:27:54,740] [INFO] Task succeeded: HMMsearch
[2023-06-13 14:27:54,741] [INFO] Found 6/6 markers.
[2023-06-13 14:27:54,808] [INFO] Query marker FASTA was written to GCA_022744865.1_ASM2274486v1_genomic.fna/markers.fasta
[2023-06-13 14:27:54,809] [INFO] Task started: Blastn
[2023-06-13 14:27:54,809] [INFO] Running command: blastn -query GCA_022744865.1_ASM2274486v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ecb4e96-ffba-4e75-b33b-3fc50d314a51/dqc_reference/reference_markers.fasta -out GCA_022744865.1_ASM2274486v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:27:55,547] [INFO] Task succeeded: Blastn
[2023-06-13 14:27:55,552] [INFO] Selected 21 target genomes.
[2023-06-13 14:27:55,552] [INFO] Target genome list was writen to GCA_022744865.1_ASM2274486v1_genomic.fna/target_genomes.txt
[2023-06-13 14:27:55,553] [INFO] Task started: fastANI
[2023-06-13 14:27:55,553] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2de6ee4-5604-422d-b4e0-2ccad435a5d8/GCA_022744865.1_ASM2274486v1_genomic.fna.gz --refList GCA_022744865.1_ASM2274486v1_genomic.fna/target_genomes.txt --output GCA_022744865.1_ASM2274486v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 14:28:07,269] [INFO] Task succeeded: fastANI
[2023-06-13 14:28:07,269] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ecb4e96-ffba-4e75-b33b-3fc50d314a51/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 14:28:07,269] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ecb4e96-ffba-4e75-b33b-3fc50d314a51/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 14:28:07,284] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2023-06-13 14:28:07,284] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 14:28:07,285] [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
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	96.8436	664	845	95	conclusive
Prevotella pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	78.5215	163	845	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	78.3139	129	845	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	78.2875	131	845	95	below_threshold
Prevotella hominis	strain=BCRC 81118	GCA_004535825.1	2518605	2518605	type	True	78.181	118	845	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	78.1674	127	845	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	77.8511	132	845	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	77.386	91	845	95	below_threshold
Prevotella illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	77.3296	55	845	95	below_threshold
Prevotella lascolaii	strain=khD1	GCA_900079775.1	1776379	1776379	type	True	77.2949	154	845	95	below_threshold
Palleniella intestinalis	strain=PINT	GCA_013166595.1	2736291	2736291	type	True	77.1712	65	845	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	77.0697	89	845	95	below_threshold
Prevotella ruminicola	strain=Bryant 23	GCA_000025925.1	839	839	type	True	77.0409	90	845	95	below_threshold
Prevotella falsenii	strain=JCM 15124	GCA_000613945.1	515414	515414	type	True	77.0011	53	845	95	below_threshold
Prevotella ruminicola	strain=ATCC 19189	GCA_900108375.1	839	839	type	True	76.9669	90	845	95	below_threshold
Prevotella loescheii	strain=DSM 19665	GCA_000378085.1	840	840	type	True	76.8078	54	845	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 14:28:07,289] [INFO] DFAST Taxonomy check result was written to GCA_022744865.1_ASM2274486v1_genomic.fna/tc_result.tsv
[2023-06-13 14:28:07,291] [INFO] ===== Taxonomy check completed =====
[2023-06-13 14:28:07,292] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 14:28:07,292] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ecb4e96-ffba-4e75-b33b-3fc50d314a51/dqc_reference/checkm_data
[2023-06-13 14:28:07,293] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 14:28:07,341] [INFO] Task started: CheckM
[2023-06-13 14:28:07,341] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022744865.1_ASM2274486v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022744865.1_ASM2274486v1_genomic.fna/checkm_input GCA_022744865.1_ASM2274486v1_genomic.fna/checkm_result
[2023-06-13 14:28:56,510] [INFO] Task succeeded: CheckM
[2023-06-13 14:28:56,512] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 16.48%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 14:28:56,540] [INFO] ===== Completeness check finished =====
[2023-06-13 14:28:56,540] [INFO] ===== Start GTDB Search =====
[2023-06-13 14:28:56,541] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022744865.1_ASM2274486v1_genomic.fna/markers.fasta)
[2023-06-13 14:28:56,541] [INFO] Task started: Blastn
[2023-06-13 14:28:56,541] [INFO] Running command: blastn -query GCA_022744865.1_ASM2274486v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ecb4e96-ffba-4e75-b33b-3fc50d314a51/dqc_reference/reference_markers_gtdb.fasta -out GCA_022744865.1_ASM2274486v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:28:57,451] [INFO] Task succeeded: Blastn
[2023-06-13 14:28:57,471] [INFO] Selected 11 target genomes.
[2023-06-13 14:28:57,471] [INFO] Target genome list was writen to GCA_022744865.1_ASM2274486v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 14:28:57,473] [INFO] Task started: fastANI
[2023-06-13 14:28:57,473] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2de6ee4-5604-422d-b4e0-2ccad435a5d8/GCA_022744865.1_ASM2274486v1_genomic.fna.gz --refList GCA_022744865.1_ASM2274486v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022744865.1_ASM2274486v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 14:29:03,573] [INFO] Task succeeded: fastANI
[2023-06-13 14:29:03,589] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 14:29:03,589] [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_000235885.1	s__Prevotella stercorea	96.8436	664	845	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.02	96.84	0.81	0.69	8	conclusive
GCF_019052365.1	s__Prevotella sp000434975	89.4845	585	845	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.22	96.59	0.82	0.74	11	-
GCA_900550035.1	s__Prevotella sp900550035	80.9496	368	845	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.97	99.93	0.97	0.97	3	-
GCA_002490315.1	s__Prevotella sp002490315	80.7527	288	845	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002265625.1	s__Prevotella sp002265625	80.6656	399	845	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.90	96.80	0.88	0.86	4	-
GCA_900552515.1	s__Prevotella sp900552515	80.499	279	845	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.61	97.50	0.85	0.85	3	-
GCA_900553155.1	s__Prevotella sp900553155	80.3147	225	845	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.04	96.93	0.80	0.75	3	-
GCA_900544495.1	s__Prevotella sp900544495	79.942	345	845	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.45	98.42	0.86	0.82	3	-
GCA_900546575.1	s__Prevotella sp900546575	79.8375	334	845	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.21	95.49	0.86	0.86	4	-
GCA_900552675.1	s__Prevotella sp900552675	77.9352	110	845	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.55	95.81	0.80	0.75	5	-
--------------------------------------------------------------------------------
[2023-06-13 14:29:03,592] [INFO] GTDB search result was written to GCA_022744865.1_ASM2274486v1_genomic.fna/result_gtdb.tsv
[2023-06-13 14:29:03,592] [INFO] ===== GTDB Search completed =====
[2023-06-13 14:29:03,596] [INFO] DFAST_QC result json was written to GCA_022744865.1_ASM2274486v1_genomic.fna/dqc_result.json
[2023-06-13 14:29:03,596] [INFO] DFAST_QC completed!
[2023-06-13 14:29:03,596] [INFO] Total running time: 0h1m29s