[2024-01-24 13:55:45,856] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:45,858] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:45,859] [INFO] DQC Reference Directory: /var/lib/cwl/stg47d5f9fc-374d-4339-a098-0bbd20b62733/dqc_reference
[2024-01-24 13:55:47,080] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:47,081] [INFO] Task started: Prodigal
[2024-01-24 13:55:47,081] [INFO] Running command: gunzip -c /var/lib/cwl/stgedd33cc0-8d0b-4331-a8da-5e02bf58401a/GCF_014287575.1_ASM1428757v1_genomic.fna.gz | prodigal -d GCF_014287575.1_ASM1428757v1_genomic.fna/cds.fna -a GCF_014287575.1_ASM1428757v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:11,242] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:11,243] [INFO] Task started: HMMsearch
[2024-01-24 13:56:11,243] [INFO] Running command: hmmsearch --tblout GCF_014287575.1_ASM1428757v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg47d5f9fc-374d-4339-a098-0bbd20b62733/dqc_reference/reference_markers.hmm GCF_014287575.1_ASM1428757v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:11,530] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:11,532] [INFO] Found 6/6 markers.
[2024-01-24 13:56:11,568] [INFO] Query marker FASTA was written to GCF_014287575.1_ASM1428757v1_genomic.fna/markers.fasta
[2024-01-24 13:56:11,568] [INFO] Task started: Blastn
[2024-01-24 13:56:11,568] [INFO] Running command: blastn -query GCF_014287575.1_ASM1428757v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47d5f9fc-374d-4339-a098-0bbd20b62733/dqc_reference/reference_markers.fasta -out GCF_014287575.1_ASM1428757v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:12,191] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:12,195] [INFO] Selected 10 target genomes.
[2024-01-24 13:56:12,196] [INFO] Target genome list was writen to GCF_014287575.1_ASM1428757v1_genomic.fna/target_genomes.txt
[2024-01-24 13:56:12,198] [INFO] Task started: fastANI
[2024-01-24 13:56:12,198] [INFO] Running command: fastANI --query /var/lib/cwl/stgedd33cc0-8d0b-4331-a8da-5e02bf58401a/GCF_014287575.1_ASM1428757v1_genomic.fna.gz --refList GCF_014287575.1_ASM1428757v1_genomic.fna/target_genomes.txt --output GCF_014287575.1_ASM1428757v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:21,591] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:21,592] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg47d5f9fc-374d-4339-a098-0bbd20b62733/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:21,592] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg47d5f9fc-374d-4339-a098-0bbd20b62733/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:21,603] [INFO] Found 9 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 13:56:21,603] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:56:21,603] [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 humanifaecis	strain=KGMB07931	GCA_017309675.2	2792859	2792859	type	True	99.106	1225	1375	95	inconclusive
Bacteroides uniformis	strain=FDAARGOS_901	GCA_016117815.1	820	820	type	True	95.9187	1072	1375	95	inconclusive
Bacteroides uniformis	strain=DSM 6597	GCA_900107315.1	820	820	type	True	95.8936	1068	1375	95	inconclusive
Bacteroides uniformis	strain=ATCC 8492	GCA_000154205.1	820	820	type	True	95.8773	1070	1375	95	inconclusive
Bacteroides uniformis	strain=ATCC 8492	GCA_025147485.1	820	820	type	True	95.8345	1073	1375	95	inconclusive
Bacteroides rodentium	strain=JCM 16496	GCA_000614125.1	691816	691816	type	True	94.1225	971	1375	95	below_threshold
Bacteroides muris	strain=KH365_2	GCA_024704915.1	2937417	2937417	type	True	91.9672	888	1375	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_025147325.1	46506	46506	suspected-type	True	80.7892	576	1375	95	below_threshold
Bacteroides propionicigenes	strain=NSJ-90	GCA_018390535.1	2834112	2834112	type	True	80.6668	543	1375	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:21,605] [INFO] DFAST Taxonomy check result was written to GCF_014287575.1_ASM1428757v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:21,606] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:21,606] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:21,606] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg47d5f9fc-374d-4339-a098-0bbd20b62733/dqc_reference/checkm_data
[2024-01-24 13:56:21,608] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:21,649] [INFO] Task started: CheckM
[2024-01-24 13:56:21,649] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014287575.1_ASM1428757v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014287575.1_ASM1428757v1_genomic.fna/checkm_input GCF_014287575.1_ASM1428757v1_genomic.fna/checkm_result
[2024-01-24 13:57:26,787] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:26,789] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:26,810] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:26,810] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:26,811] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014287575.1_ASM1428757v1_genomic.fna/markers.fasta)
[2024-01-24 13:57:26,811] [INFO] Task started: Blastn
[2024-01-24 13:57:26,811] [INFO] Running command: blastn -query GCF_014287575.1_ASM1428757v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47d5f9fc-374d-4339-a098-0bbd20b62733/dqc_reference/reference_markers_gtdb.fasta -out GCF_014287575.1_ASM1428757v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:27,756] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:27,760] [INFO] Selected 14 target genomes.
[2024-01-24 13:57:27,761] [INFO] Target genome list was writen to GCF_014287575.1_ASM1428757v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:27,782] [INFO] Task started: fastANI
[2024-01-24 13:57:27,783] [INFO] Running command: fastANI --query /var/lib/cwl/stgedd33cc0-8d0b-4331-a8da-5e02bf58401a/GCF_014287575.1_ASM1428757v1_genomic.fna.gz --refList GCF_014287575.1_ASM1428757v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014287575.1_ASM1428757v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:57:39,686] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:39,701] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:57:39,701] [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	95.8773	1070	1375	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	94.1225	971	1375	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	91.7507	881	1375	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	87.6311	632	1375	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	81.8513	672	1375	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	81.49	674	1375	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	80.8642	536	1375	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	80.7909	508	1375	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000154525.1	s__Bacteroides stercoris	80.7515	582	1375	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.24	97.39	0.79	0.69	73	-
GCF_000374365.1	s__Bacteroides gallinarum	80.4108	548	1375	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.97	99.97	1.00	1.00	2	-
GCF_019129285.1	s__Bacteroides sp900552405	79.7328	534	1375	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.09	95.34	0.92	0.76	12	-
GCF_004342845.1	s__Bacteroides heparinolyticus	79.7159	500	1375	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.64	97.08	0.84	0.81	4	-
GCA_905198575.1	s__Phocaeicola sp905198575	77.4289	78	1375	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:57:39,705] [INFO] GTDB search result was written to GCF_014287575.1_ASM1428757v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:57:39,705] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:57:39,711] [INFO] DFAST_QC result json was written to GCF_014287575.1_ASM1428757v1_genomic.fna/dqc_result.json
[2024-01-24 13:57:39,712] [INFO] DFAST_QC completed!
[2024-01-24 13:57:39,712] [INFO] Total running time: 0h1m54s