[2024-01-24 13:40:55,164] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:55,166] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:55,166] [INFO] DQC Reference Directory: /var/lib/cwl/stg76820c87-848f-4213-ae0a-a7db23f9bd7b/dqc_reference
[2024-01-24 13:40:56,629] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:56,630] [INFO] Task started: Prodigal
[2024-01-24 13:40:56,631] [INFO] Running command: gunzip -c /var/lib/cwl/stge442f434-00d3-4527-b764-626951ef49a7/GCF_014288065.1_ASM1428806v1_genomic.fna.gz | prodigal -d GCF_014288065.1_ASM1428806v1_genomic.fna/cds.fna -a GCF_014288065.1_ASM1428806v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:02,491] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:02,491] [INFO] Task started: HMMsearch
[2024-01-24 13:41:02,491] [INFO] Running command: hmmsearch --tblout GCF_014288065.1_ASM1428806v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg76820c87-848f-4213-ae0a-a7db23f9bd7b/dqc_reference/reference_markers.hmm GCF_014288065.1_ASM1428806v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:02,767] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:02,768] [INFO] Found 6/6 markers.
[2024-01-24 13:41:02,791] [INFO] Query marker FASTA was written to GCF_014288065.1_ASM1428806v1_genomic.fna/markers.fasta
[2024-01-24 13:41:02,792] [INFO] Task started: Blastn
[2024-01-24 13:41:02,792] [INFO] Running command: blastn -query GCF_014288065.1_ASM1428806v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg76820c87-848f-4213-ae0a-a7db23f9bd7b/dqc_reference/reference_markers.fasta -out GCF_014288065.1_ASM1428806v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:03,480] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:03,484] [INFO] Selected 20 target genomes.
[2024-01-24 13:41:03,484] [INFO] Target genome list was writen to GCF_014288065.1_ASM1428806v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:03,491] [INFO] Task started: fastANI
[2024-01-24 13:41:03,492] [INFO] Running command: fastANI --query /var/lib/cwl/stge442f434-00d3-4527-b764-626951ef49a7/GCF_014288065.1_ASM1428806v1_genomic.fna.gz --refList GCF_014288065.1_ASM1428806v1_genomic.fna/target_genomes.txt --output GCF_014288065.1_ASM1428806v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:17,580] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:17,580] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg76820c87-848f-4213-ae0a-a7db23f9bd7b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:17,581] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg76820c87-848f-4213-ae0a-a7db23f9bd7b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:17,585] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:41:17,585] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:41:17,585] [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
Ruminococcus bromii	strain=ATCC 27255	GCA_002834225.1	40518	40518	suspected-type	True	80.3519	276	804	95	below_threshold
Ruminococcus bovis	strain=JE7A12	GCA_005601135.1	2564099	2564099	type	True	76.9901	99	804	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:17,587] [INFO] DFAST Taxonomy check result was written to GCF_014288065.1_ASM1428806v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:17,587] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:17,588] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:17,588] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg76820c87-848f-4213-ae0a-a7db23f9bd7b/dqc_reference/checkm_data
[2024-01-24 13:41:17,589] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:17,628] [INFO] Task started: CheckM
[2024-01-24 13:41:17,628] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014288065.1_ASM1428806v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014288065.1_ASM1428806v1_genomic.fna/checkm_input GCF_014288065.1_ASM1428806v1_genomic.fna/checkm_result
[2024-01-24 13:41:41,870] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:41,871] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:41,895] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:41,896] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:41,896] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014288065.1_ASM1428806v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:41,896] [INFO] Task started: Blastn
[2024-01-24 13:41:41,896] [INFO] Running command: blastn -query GCF_014288065.1_ASM1428806v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg76820c87-848f-4213-ae0a-a7db23f9bd7b/dqc_reference/reference_markers_gtdb.fasta -out GCF_014288065.1_ASM1428806v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:43,000] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:43,004] [INFO] Selected 14 target genomes.
[2024-01-24 13:41:43,004] [INFO] Target genome list was writen to GCF_014288065.1_ASM1428806v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:43,043] [INFO] Task started: fastANI
[2024-01-24 13:41:43,044] [INFO] Running command: fastANI --query /var/lib/cwl/stge442f434-00d3-4527-b764-626951ef49a7/GCF_014288065.1_ASM1428806v1_genomic.fna.gz --refList GCF_014288065.1_ASM1428806v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014288065.1_ASM1428806v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:50,159] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:50,170] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:50,170] [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_014288065.1	s__Ruminococcus_E sp003526955	100.0	803	804	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	97.97	97.37	0.85	0.74	16	conclusive
GCF_003438075.1	s__Ruminococcus_E sp003438075	90.8726	610	804	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	98.49	97.62	0.94	0.88	5	-
GCA_900755995.1	s__Ruminococcus_E sp900755995	82.3179	390	804	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002834235.1	s__Ruminococcus_E bromii_B	81.9688	328	804	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	97.64	96.93	0.86	0.80	74	-
GCA_902771755.1	s__Ruminococcus_E sp902771755	79.4785	226	804	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101355.1	s__Ruminococcus_E bromii_A	79.2455	213	804	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	99.01	98.16	0.84	0.65	5	-
GCA_002493635.1	s__Ruminococcus_E sp002493635	79.0677	181	804	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	98.92	97.46	0.88	0.85	4	-
GCA_902766775.1	s__Ruminococcus_E sp902766775	79.0534	223	804	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003521625.1	s__Ruminococcus_E sp003521625	78.8453	190	804	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002491825.1	s__Ruminococcus_E sp002491825	78.7912	150	804	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902766885.1	s__Ruminococcus_E sp902766885	78.5393	218	804	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900543095.1	s__Ruminococcus_E sp900543095	78.2525	159	804	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	99.93	99.93	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:50,172] [INFO] GTDB search result was written to GCF_014288065.1_ASM1428806v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:50,173] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:50,176] [INFO] DFAST_QC result json was written to GCF_014288065.1_ASM1428806v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:50,177] [INFO] DFAST_QC completed!
[2024-01-24 13:41:50,177] [INFO] Total running time: 0h0m55s