[2023-06-29 14:35:14,293] [INFO] DFAST_QC pipeline started.
[2023-06-29 14:35:14,295] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 14:35:14,295] [INFO] DQC Reference Directory: /var/lib/cwl/stg37511961-5ef4-499f-a1ed-7f777a4a85f7/dqc_reference
[2023-06-29 14:35:15,572] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 14:35:15,573] [INFO] Task started: Prodigal
[2023-06-29 14:35:15,573] [INFO] Running command: gunzip -c /var/lib/cwl/stgdcf1c4af-a23e-4987-80e4-0cc3c3c4b30b/GCA_021153065.1_ASM2115306v1_genomic.fna.gz | prodigal -d GCA_021153065.1_ASM2115306v1_genomic.fna/cds.fna -a GCA_021153065.1_ASM2115306v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 14:35:45,682] [INFO] Task succeeded: Prodigal
[2023-06-29 14:35:45,683] [INFO] Task started: HMMsearch
[2023-06-29 14:35:45,683] [INFO] Running command: hmmsearch --tblout GCA_021153065.1_ASM2115306v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg37511961-5ef4-499f-a1ed-7f777a4a85f7/dqc_reference/reference_markers.hmm GCA_021153065.1_ASM2115306v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 14:35:46,008] [INFO] Task succeeded: HMMsearch
[2023-06-29 14:35:46,010] [INFO] Found 6/6 markers.
[2023-06-29 14:35:46,056] [INFO] Query marker FASTA was written to GCA_021153065.1_ASM2115306v1_genomic.fna/markers.fasta
[2023-06-29 14:35:46,057] [INFO] Task started: Blastn
[2023-06-29 14:35:46,057] [INFO] Running command: blastn -query GCA_021153065.1_ASM2115306v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg37511961-5ef4-499f-a1ed-7f777a4a85f7/dqc_reference/reference_markers.fasta -out GCA_021153065.1_ASM2115306v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:35:46,701] [INFO] Task succeeded: Blastn
[2023-06-29 14:35:46,707] [INFO] Selected 11 target genomes.
[2023-06-29 14:35:46,708] [INFO] Target genome list was writen to GCA_021153065.1_ASM2115306v1_genomic.fna/target_genomes.txt
[2023-06-29 14:35:46,709] [INFO] Task started: fastANI
[2023-06-29 14:35:46,710] [INFO] Running command: fastANI --query /var/lib/cwl/stgdcf1c4af-a23e-4987-80e4-0cc3c3c4b30b/GCA_021153065.1_ASM2115306v1_genomic.fna.gz --refList GCA_021153065.1_ASM2115306v1_genomic.fna/target_genomes.txt --output GCA_021153065.1_ASM2115306v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 14:35:57,290] [INFO] Task succeeded: fastANI
[2023-06-29 14:35:57,291] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg37511961-5ef4-499f-a1ed-7f777a4a85f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 14:35:57,291] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg37511961-5ef4-499f-a1ed-7f777a4a85f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 14:35:57,302] [INFO] Found 10 fastANI hits (5 hits with ANI > threshold)
[2023-06-29 14:35:57,302] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2023-06-29 14:35:57,302] [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
Bacteroides uniformis	strain=DSM 6597	GCA_900107315.1	820	820	type	True	98.2591	1147	1623	95	inconclusive
Bacteroides uniformis	strain=FDAARGOS_901	GCA_016117815.1	820	820	type	True	98.1955	1164	1623	95	inconclusive
Bacteroides uniformis	strain=ATCC 8492	GCA_025147485.1	820	820	type	True	98.1858	1151	1623	95	inconclusive
Bacteroides uniformis	strain=ATCC 8492	GCA_000154205.1	820	820	type	True	98.1848	1155	1623	95	inconclusive
Bacteroides humanifaecis	strain=KGMB07931	GCA_017309675.2	2792859	2792859	type	True	95.7742	1046	1623	95	inconclusive
Bacteroides rodentium	strain=JCM 16496	GCA_000614125.1	691816	691816	type	True	94.2533	1005	1623	95	below_threshold
Bacteroides muris	strain=KH365_2	GCA_024704915.1	2937417	2937417	type	True	92.1951	854	1623	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_025147325.1	46506	46506	suspected-type	True	81.6788	578	1623	95	below_threshold
Bacteroides propionicigenes	strain=NSJ-90	GCA_018390535.1	2834112	2834112	type	True	81.1398	576	1623	95	below_threshold
Bacteroides stercorirosoris	strain=JCM 17103	GCA_000614165.1	871324	871324	type	True	80.9344	564	1623	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 14:35:57,305] [INFO] DFAST Taxonomy check result was written to GCA_021153065.1_ASM2115306v1_genomic.fna/tc_result.tsv
[2023-06-29 14:35:57,305] [INFO] ===== Taxonomy check completed =====
[2023-06-29 14:35:57,305] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 14:35:57,305] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg37511961-5ef4-499f-a1ed-7f777a4a85f7/dqc_reference/checkm_data
[2023-06-29 14:35:57,306] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 14:35:57,357] [INFO] Task started: CheckM
[2023-06-29 14:35:57,357] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021153065.1_ASM2115306v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021153065.1_ASM2115306v1_genomic.fna/checkm_input GCA_021153065.1_ASM2115306v1_genomic.fna/checkm_result
[2023-06-29 14:37:18,554] [INFO] Task succeeded: CheckM
[2023-06-29 14:37:18,555] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-29 14:37:18,580] [INFO] ===== Completeness check finished =====
[2023-06-29 14:37:18,580] [INFO] ===== Start GTDB Search =====
[2023-06-29 14:37:18,581] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021153065.1_ASM2115306v1_genomic.fna/markers.fasta)
[2023-06-29 14:37:18,581] [INFO] Task started: Blastn
[2023-06-29 14:37:18,581] [INFO] Running command: blastn -query GCA_021153065.1_ASM2115306v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg37511961-5ef4-499f-a1ed-7f777a4a85f7/dqc_reference/reference_markers_gtdb.fasta -out GCA_021153065.1_ASM2115306v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:37:19,459] [INFO] Task succeeded: Blastn
[2023-06-29 14:37:19,464] [INFO] Selected 12 target genomes.
[2023-06-29 14:37:19,464] [INFO] Target genome list was writen to GCA_021153065.1_ASM2115306v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 14:37:19,466] [INFO] Task started: fastANI
[2023-06-29 14:37:19,466] [INFO] Running command: fastANI --query /var/lib/cwl/stgdcf1c4af-a23e-4987-80e4-0cc3c3c4b30b/GCA_021153065.1_ASM2115306v1_genomic.fna.gz --refList GCA_021153065.1_ASM2115306v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021153065.1_ASM2115306v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 14:37:29,432] [INFO] Task succeeded: fastANI
[2023-06-29 14:37:29,448] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 14:37:29,448] [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_000154205.1	s__Bacteroides uniformis	98.2052	1154	1623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.42	95.87	0.83	0.69	301	conclusive
GCF_000614125.1	s__Bacteroides rodentium	94.2565	1005	1623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004793475.1	s__Bacteroides sp002491635	91.7337	880	1623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.51	98.46	0.94	0.83	13	-
GCA_905197435.1	s__Bacteroides sp905197435	88.1962	630	1623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000195635.1	s__Bacteroides fluxus	82.7179	672	1623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.66	99.32	0.94	0.88	3	-
GCA_902388495.1	s__Bacteroides sp902388495	81.6919	663	1623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.99	99.99	0.98	0.98	2	-
GCF_003438615.1	s__Bacteroides sp003545565	81.6498	553	1623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.56	99.02	0.91	0.88	7	-
GCA_905203765.1	s__Bacteroides sp905203765	81.0801	489	1623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374365.1	s__Bacteroides gallinarum	80.3653	556	1623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.97	99.97	1.00	1.00	2	-
GCF_000186225.1	s__Bacteroides helcogenes	80.0457	522	1623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905198575.1	s__Phocaeicola sp905198575	77.7183	74	1623	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 14:37:29,451] [INFO] GTDB search result was written to GCA_021153065.1_ASM2115306v1_genomic.fna/result_gtdb.tsv
[2023-06-29 14:37:29,451] [INFO] ===== GTDB Search completed =====
[2023-06-29 14:37:29,455] [INFO] DFAST_QC result json was written to GCA_021153065.1_ASM2115306v1_genomic.fna/dqc_result.json
[2023-06-29 14:37:29,455] [INFO] DFAST_QC completed!
[2023-06-29 14:37:29,456] [INFO] Total running time: 0h2m15s