[2023-06-28 06:25:52,597] [INFO] DFAST_QC pipeline started.
[2023-06-28 06:25:52,599] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 06:25:52,599] [INFO] DQC Reference Directory: /var/lib/cwl/stg65af32b8-e3d9-49d7-870b-95677c57e8f6/dqc_reference
[2023-06-28 06:25:53,838] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 06:25:53,839] [INFO] Task started: Prodigal
[2023-06-28 06:25:53,839] [INFO] Running command: gunzip -c /var/lib/cwl/stg3cc1ce54-9d29-4776-b199-1aee5ea1707d/GCA_017558025.1_ASM1755802v1_genomic.fna.gz | prodigal -d GCA_017558025.1_ASM1755802v1_genomic.fna/cds.fna -a GCA_017558025.1_ASM1755802v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 06:26:05,445] [INFO] Task succeeded: Prodigal
[2023-06-28 06:26:05,446] [INFO] Task started: HMMsearch
[2023-06-28 06:26:05,446] [INFO] Running command: hmmsearch --tblout GCA_017558025.1_ASM1755802v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg65af32b8-e3d9-49d7-870b-95677c57e8f6/dqc_reference/reference_markers.hmm GCA_017558025.1_ASM1755802v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 06:26:05,710] [INFO] Task succeeded: HMMsearch
[2023-06-28 06:26:05,712] [INFO] Found 6/6 markers.
[2023-06-28 06:26:05,737] [INFO] Query marker FASTA was written to GCA_017558025.1_ASM1755802v1_genomic.fna/markers.fasta
[2023-06-28 06:26:05,738] [INFO] Task started: Blastn
[2023-06-28 06:26:05,738] [INFO] Running command: blastn -query GCA_017558025.1_ASM1755802v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg65af32b8-e3d9-49d7-870b-95677c57e8f6/dqc_reference/reference_markers.fasta -out GCA_017558025.1_ASM1755802v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 06:26:06,332] [INFO] Task succeeded: Blastn
[2023-06-28 06:26:06,336] [INFO] Selected 22 target genomes.
[2023-06-28 06:26:06,337] [INFO] Target genome list was writen to GCA_017558025.1_ASM1755802v1_genomic.fna/target_genomes.txt
[2023-06-28 06:26:06,338] [INFO] Task started: fastANI
[2023-06-28 06:26:06,338] [INFO] Running command: fastANI --query /var/lib/cwl/stg3cc1ce54-9d29-4776-b199-1aee5ea1707d/GCA_017558025.1_ASM1755802v1_genomic.fna.gz --refList GCA_017558025.1_ASM1755802v1_genomic.fna/target_genomes.txt --output GCA_017558025.1_ASM1755802v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 06:26:18,832] [INFO] Task succeeded: fastANI
[2023-06-28 06:26:18,833] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg65af32b8-e3d9-49d7-870b-95677c57e8f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 06:26:18,833] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg65af32b8-e3d9-49d7-870b-95677c57e8f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 06:26:18,840] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 06:26:18,841] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 06:26:18,841] [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 provencensis	strain=Marseille-P2431	GCA_900083545.1	1816676	1816676	type	True	76.7601	59	656	95	below_threshold
Alistipes senegalensis	strain=FDAARGOS_1578	GCA_020735725.1	1288121	1288121	type	True	76.4205	64	656	95	below_threshold
Alistipes senegalensis	strain=JC50	GCA_025145645.1	1288121	1288121	type	True	76.3374	61	656	95	below_threshold
Alistipes senegalensis	strain=JC50	GCA_000312145.1	1288121	1288121	type	True	76.2963	61	656	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_000210575.1	328814	328814	suspected-type	True	76.1888	66	656	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 06:26:18,843] [INFO] DFAST Taxonomy check result was written to GCA_017558025.1_ASM1755802v1_genomic.fna/tc_result.tsv
[2023-06-28 06:26:18,843] [INFO] ===== Taxonomy check completed =====
[2023-06-28 06:26:18,844] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 06:26:18,844] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg65af32b8-e3d9-49d7-870b-95677c57e8f6/dqc_reference/checkm_data
[2023-06-28 06:26:18,846] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 06:26:18,875] [INFO] Task started: CheckM
[2023-06-28 06:26:18,875] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017558025.1_ASM1755802v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017558025.1_ASM1755802v1_genomic.fna/checkm_input GCA_017558025.1_ASM1755802v1_genomic.fna/checkm_result
[2023-06-28 06:26:55,946] [INFO] Task succeeded: CheckM
[2023-06-28 06:26:55,948] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.77%
Strain heterogeneity: 40.00%
--------------------------------------------------------------------------------
[2023-06-28 06:26:55,971] [INFO] ===== Completeness check finished =====
[2023-06-28 06:26:55,971] [INFO] ===== Start GTDB Search =====
[2023-06-28 06:26:55,972] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017558025.1_ASM1755802v1_genomic.fna/markers.fasta)
[2023-06-28 06:26:55,972] [INFO] Task started: Blastn
[2023-06-28 06:26:55,972] [INFO] Running command: blastn -query GCA_017558025.1_ASM1755802v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg65af32b8-e3d9-49d7-870b-95677c57e8f6/dqc_reference/reference_markers_gtdb.fasta -out GCA_017558025.1_ASM1755802v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 06:26:56,792] [INFO] Task succeeded: Blastn
[2023-06-28 06:26:56,797] [INFO] Selected 17 target genomes.
[2023-06-28 06:26:56,797] [INFO] Target genome list was writen to GCA_017558025.1_ASM1755802v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 06:26:56,802] [INFO] Task started: fastANI
[2023-06-28 06:26:56,803] [INFO] Running command: fastANI --query /var/lib/cwl/stg3cc1ce54-9d29-4776-b199-1aee5ea1707d/GCA_017558025.1_ASM1755802v1_genomic.fna.gz --refList GCA_017558025.1_ASM1755802v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017558025.1_ASM1755802v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 06:27:03,930] [INFO] Task succeeded: fastANI
[2023-06-28 06:27:03,949] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 06:27:03,950] [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_017631255.1	s__Alistipes sp017631255	95.5628	533	656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	95.67	95.65	0.90	0.88	4	conclusive
GCA_017465055.1	s__Alistipes sp017465055	81.5652	381	656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017630455.1	s__Alistipes sp017630455	81.0564	356	656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904502285.1	s__Alistipes sp904502285	80.8845	338	656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	100.00	100.00	1.00	1.00	2	-
GCA_015059715.1	s__Alistipes sp015059715	80.8319	390	656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017559615.1	s__Alistipes sp017559615	80.6991	337	656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	95.64	95.64	0.85	0.85	3	-
GCA_900768015.1	s__Alistipes sp900768015	80.6379	353	656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	95.92	95.92	0.89	0.89	2	-
GCA_017380955.1	s__Alistipes sp017380955	80.5121	275	656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017621455.1	s__Alistipes sp017621455	80.4996	309	656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017937765.1	s__Alistipes sp017937765	80.3997	345	656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900769445.1	s__Alistipes sp900769445	80.3537	274	656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017647625.1	s__Alistipes sp017647625	80.3075	286	656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.38	98.38	0.79	0.79	2	-
GCA_900770635.1	s__Alistipes sp900770635	80.2004	301	656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	97.57	97.53	0.93	0.91	3	-
GCA_900768045.1	s__Alistipes sp900768045	79.9421	290	656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017558115.1	s__Alistipes sp017558115	79.9012	315	656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017559425.1	s__Alistipes sp017559425	79.7878	284	656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017631135.1	s__Alistipes sp017631135	78.6839	205	656	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 06:27:03,959] [INFO] GTDB search result was written to GCA_017558025.1_ASM1755802v1_genomic.fna/result_gtdb.tsv
[2023-06-28 06:27:03,959] [INFO] ===== GTDB Search completed =====
[2023-06-28 06:27:03,964] [INFO] DFAST_QC result json was written to GCA_017558025.1_ASM1755802v1_genomic.fna/dqc_result.json
[2023-06-28 06:27:03,965] [INFO] DFAST_QC completed!
[2023-06-28 06:27:03,965] [INFO] Total running time: 0h1m11s