[2023-06-30 20:21:29,817] [INFO] DFAST_QC pipeline started.
[2023-06-30 20:21:29,831] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 20:21:29,831] [INFO] DQC Reference Directory: /var/lib/cwl/stg50cba038-8deb-48d0-aa21-5dc2cf85a394/dqc_reference
[2023-06-30 20:21:31,718] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 20:21:31,719] [INFO] Task started: Prodigal
[2023-06-30 20:21:31,719] [INFO] Running command: gunzip -c /var/lib/cwl/stg40957762-5a8a-491a-ac7f-ce14725394e8/GCA_024331085.1_ASM2433108v1_genomic.fna.gz | prodigal -d GCA_024331085.1_ASM2433108v1_genomic.fna/cds.fna -a GCA_024331085.1_ASM2433108v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 20:21:39,087] [INFO] Task succeeded: Prodigal
[2023-06-30 20:21:39,087] [INFO] Task started: HMMsearch
[2023-06-30 20:21:39,087] [INFO] Running command: hmmsearch --tblout GCA_024331085.1_ASM2433108v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg50cba038-8deb-48d0-aa21-5dc2cf85a394/dqc_reference/reference_markers.hmm GCA_024331085.1_ASM2433108v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 20:21:39,255] [INFO] Task succeeded: HMMsearch
[2023-06-30 20:21:39,256] [INFO] Found 6/6 markers.
[2023-06-30 20:21:39,282] [INFO] Query marker FASTA was written to GCA_024331085.1_ASM2433108v1_genomic.fna/markers.fasta
[2023-06-30 20:21:39,282] [INFO] Task started: Blastn
[2023-06-30 20:21:39,282] [INFO] Running command: blastn -query GCA_024331085.1_ASM2433108v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg50cba038-8deb-48d0-aa21-5dc2cf85a394/dqc_reference/reference_markers.fasta -out GCA_024331085.1_ASM2433108v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 20:21:39,876] [INFO] Task succeeded: Blastn
[2023-06-30 20:21:39,880] [INFO] Selected 13 target genomes.
[2023-06-30 20:21:39,880] [INFO] Target genome list was writen to GCA_024331085.1_ASM2433108v1_genomic.fna/target_genomes.txt
[2023-06-30 20:21:39,881] [INFO] Task started: fastANI
[2023-06-30 20:21:39,881] [INFO] Running command: fastANI --query /var/lib/cwl/stg40957762-5a8a-491a-ac7f-ce14725394e8/GCA_024331085.1_ASM2433108v1_genomic.fna.gz --refList GCA_024331085.1_ASM2433108v1_genomic.fna/target_genomes.txt --output GCA_024331085.1_ASM2433108v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 20:21:48,564] [INFO] Task succeeded: fastANI
[2023-06-30 20:21:48,565] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg50cba038-8deb-48d0-aa21-5dc2cf85a394/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 20:21:48,565] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg50cba038-8deb-48d0-aa21-5dc2cf85a394/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 20:21:48,569] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 20:21:48,569] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 20:21:48,569] [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
Nitrospira moscoviensis	strain=NSP M-1	GCA_001273775.1	42253	42253	type	True	77.3501	152	799	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 20:21:48,571] [INFO] DFAST Taxonomy check result was written to GCA_024331085.1_ASM2433108v1_genomic.fna/tc_result.tsv
[2023-06-30 20:21:48,572] [INFO] ===== Taxonomy check completed =====
[2023-06-30 20:21:48,572] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 20:21:48,572] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg50cba038-8deb-48d0-aa21-5dc2cf85a394/dqc_reference/checkm_data
[2023-06-30 20:21:48,574] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 20:21:48,602] [INFO] Task started: CheckM
[2023-06-30 20:21:48,603] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024331085.1_ASM2433108v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024331085.1_ASM2433108v1_genomic.fna/checkm_input GCA_024331085.1_ASM2433108v1_genomic.fna/checkm_result
[2023-06-30 20:22:14,709] [INFO] Task succeeded: CheckM
[2023-06-30 20:22:14,710] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.25%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 20:22:14,728] [INFO] ===== Completeness check finished =====
[2023-06-30 20:22:14,729] [INFO] ===== Start GTDB Search =====
[2023-06-30 20:22:14,729] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024331085.1_ASM2433108v1_genomic.fna/markers.fasta)
[2023-06-30 20:22:14,729] [INFO] Task started: Blastn
[2023-06-30 20:22:14,729] [INFO] Running command: blastn -query GCA_024331085.1_ASM2433108v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg50cba038-8deb-48d0-aa21-5dc2cf85a394/dqc_reference/reference_markers_gtdb.fasta -out GCA_024331085.1_ASM2433108v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 20:22:15,731] [INFO] Task succeeded: Blastn
[2023-06-30 20:22:15,735] [INFO] Selected 17 target genomes.
[2023-06-30 20:22:15,735] [INFO] Target genome list was writen to GCA_024331085.1_ASM2433108v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 20:22:15,736] [INFO] Task started: fastANI
[2023-06-30 20:22:15,736] [INFO] Running command: fastANI --query /var/lib/cwl/stg40957762-5a8a-491a-ac7f-ce14725394e8/GCA_024331085.1_ASM2433108v1_genomic.fna.gz --refList GCA_024331085.1_ASM2433108v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024331085.1_ASM2433108v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 20:22:25,938] [INFO] Task succeeded: fastANI
[2023-06-30 20:22:25,951] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 20:22:25,951] [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_001458695.1	s__Nitrospira_F inopinata	91.4149	726	799	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__Nitrospira_F	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002451055.1	s__Nitrospira_F sp002451055	77.5101	213	799	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__Nitrospira_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001273775.1	s__Nitrospira_E moscoviensis	77.3501	152	799	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__Nitrospira_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015903945.1	s__Nitrospira_F sp015903945	77.3469	171	799	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__Nitrospira_F	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011331925.1	s__Nitrospira_F sp011331925	77.3298	102	799	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__Nitrospira_F	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005116745.1	s__Nitrospira_F sp005116745	77.2768	76	799	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__Nitrospira_F	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005239465.1	s__Nitrospira_F sp005239465	77.0946	140	799	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__Nitrospira_F	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016873455.1	s__Nitrospira_F sp016873455	77.0896	150	799	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__Nitrospira_F	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002420105.1	s__Nitrospira_C sp002420105	77.0599	127	799	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__Nitrospira_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458775.1	s__Nitrospira_F nitrificans	77.0046	121	799	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__Nitrospira_F	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900299325.1	s__OMJK01 sp900299325	76.9964	127	799	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__OMJK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015709715.1	s__Nitrospira_A sp001567445	76.885	90	799	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__Nitrospira_A	95.0	99.74	99.55	0.97	0.95	6	-
GCA_018242765.1	s__Nitrospira_F sp018242765	76.8835	89	799	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__Nitrospira_F	95.0	98.63	98.34	0.91	0.89	3	-
GCA_015903995.1	s__Nitrospira_F sp015903995	76.3218	101	799	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__Nitrospira_F	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002435325.1	s__Nitrospira_D sp002435325	76.267	90	799	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__Nitrospira_D	95.0	99.94	99.94	0.95	0.95	2	-
GCA_016222925.1	s__Nitrospira_F sp016222925	76.1216	60	799	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__Nitrospiraceae;g__Nitrospira_F	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 20:22:25,953] [INFO] GTDB search result was written to GCA_024331085.1_ASM2433108v1_genomic.fna/result_gtdb.tsv
[2023-06-30 20:22:25,954] [INFO] ===== GTDB Search completed =====
[2023-06-30 20:22:25,959] [INFO] DFAST_QC result json was written to GCA_024331085.1_ASM2433108v1_genomic.fna/dqc_result.json
[2023-06-30 20:22:25,959] [INFO] DFAST_QC completed!
[2023-06-30 20:22:25,959] [INFO] Total running time: 0h0m56s