[2024-01-25 17:41:35,572] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:41:35,575] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:41:35,575] [INFO] DQC Reference Directory: /var/lib/cwl/stg313f6f79-5a1d-429b-b4d1-8f0545b4f418/dqc_reference
[2024-01-25 17:41:36,707] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:41:36,708] [INFO] Task started: Prodigal
[2024-01-25 17:41:36,708] [INFO] Running command: gunzip -c /var/lib/cwl/stg80ad3b50-75e5-4e9b-9424-07f9a76ec8fa/GCF_000014965.1_ASM1496v1_genomic.fna.gz | prodigal -d GCF_000014965.1_ASM1496v1_genomic.fna/cds.fna -a GCF_000014965.1_ASM1496v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:41:50,310] [INFO] Task succeeded: Prodigal
[2024-01-25 17:41:50,310] [INFO] Task started: HMMsearch
[2024-01-25 17:41:50,310] [INFO] Running command: hmmsearch --tblout GCF_000014965.1_ASM1496v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg313f6f79-5a1d-429b-b4d1-8f0545b4f418/dqc_reference/reference_markers.hmm GCF_000014965.1_ASM1496v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:41:50,557] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:41:50,558] [INFO] Found 6/6 markers.
[2024-01-25 17:41:50,599] [INFO] Query marker FASTA was written to GCF_000014965.1_ASM1496v1_genomic.fna/markers.fasta
[2024-01-25 17:41:50,600] [INFO] Task started: Blastn
[2024-01-25 17:41:50,600] [INFO] Running command: blastn -query GCF_000014965.1_ASM1496v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg313f6f79-5a1d-429b-b4d1-8f0545b4f418/dqc_reference/reference_markers.fasta -out GCF_000014965.1_ASM1496v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:41:51,163] [INFO] Task succeeded: Blastn
[2024-01-25 17:41:51,165] [INFO] Selected 20 target genomes.
[2024-01-25 17:41:51,166] [INFO] Target genome list was writen to GCF_000014965.1_ASM1496v1_genomic.fna/target_genomes.txt
[2024-01-25 17:41:51,199] [INFO] Task started: fastANI
[2024-01-25 17:41:51,200] [INFO] Running command: fastANI --query /var/lib/cwl/stg80ad3b50-75e5-4e9b-9424-07f9a76ec8fa/GCF_000014965.1_ASM1496v1_genomic.fna.gz --refList GCF_000014965.1_ASM1496v1_genomic.fna/target_genomes.txt --output GCF_000014965.1_ASM1496v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:42:08,366] [INFO] Task succeeded: fastANI
[2024-01-25 17:42:08,366] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg313f6f79-5a1d-429b-b4d1-8f0545b4f418/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:42:08,367] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg313f6f79-5a1d-429b-b4d1-8f0545b4f418/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:42:08,373] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:42:08,373] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:42:08,373] [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
Syntrophobacter fumaroxidans	strain=MPOB	GCA_000014965.1	119484	119484	type	True	100.0	1659	1663	95	conclusive
Desulfoglaeba alkanexedens	strain=ALDC	GCA_005377625.1	361111	361111	type	True	76.9917	81	1663	95	below_threshold
Desulfacinum infernum	strain=DSM 9756	GCA_900129305.1	35837	35837	type	True	76.4287	97	1663	95	below_threshold
Desulfacinum hydrothermale	strain=DSM 13146	GCA_900176285.1	109258	109258	type	True	76.1301	92	1663	95	below_threshold
Desulfosarcina widdelii	strain=PP31	GCA_009688965.1	947919	947919	type	True	75.9237	56	1663	95	below_threshold
Desulfatibacillum aliphaticivorans	strain=DSM 15576	GCA_000429905.1	218208	218208	type	True	75.6248	54	1663	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:42:08,374] [INFO] DFAST Taxonomy check result was written to GCF_000014965.1_ASM1496v1_genomic.fna/tc_result.tsv
[2024-01-25 17:42:08,375] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:42:08,375] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:42:08,375] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg313f6f79-5a1d-429b-b4d1-8f0545b4f418/dqc_reference/checkm_data
[2024-01-25 17:42:08,376] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:42:08,424] [INFO] Task started: CheckM
[2024-01-25 17:42:08,424] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000014965.1_ASM1496v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000014965.1_ASM1496v1_genomic.fna/checkm_input GCF_000014965.1_ASM1496v1_genomic.fna/checkm_result
[2024-01-25 17:42:50,306] [INFO] Task succeeded: CheckM
[2024-01-25 17:42:50,307] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2024-01-25 17:42:50,331] [INFO] ===== Completeness check finished =====
[2024-01-25 17:42:50,332] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:42:50,332] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000014965.1_ASM1496v1_genomic.fna/markers.fasta)
[2024-01-25 17:42:50,332] [INFO] Task started: Blastn
[2024-01-25 17:42:50,332] [INFO] Running command: blastn -query GCF_000014965.1_ASM1496v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg313f6f79-5a1d-429b-b4d1-8f0545b4f418/dqc_reference/reference_markers_gtdb.fasta -out GCF_000014965.1_ASM1496v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:42:51,326] [INFO] Task succeeded: Blastn
[2024-01-25 17:42:51,329] [INFO] Selected 16 target genomes.
[2024-01-25 17:42:51,330] [INFO] Target genome list was writen to GCF_000014965.1_ASM1496v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:42:51,349] [INFO] Task started: fastANI
[2024-01-25 17:42:51,349] [INFO] Running command: fastANI --query /var/lib/cwl/stg80ad3b50-75e5-4e9b-9424-07f9a76ec8fa/GCF_000014965.1_ASM1496v1_genomic.fna.gz --refList GCF_000014965.1_ASM1496v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000014965.1_ASM1496v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:43:02,236] [INFO] Task succeeded: fastANI
[2024-01-25 17:43:02,245] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:43:02,246] [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_000014965.1	s__Syntrophobacter fumaroxidans	100.0	1654	1663	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__Syntrophobacteraceae;g__Syntrophobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_011328915.1	s__DSUX01 sp011328915	78.6296	137	1663	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__Syntrophobacteraceae;g__DSUX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013314815.1	s__JABUEY01 sp013314815	77.0241	161	1663	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__Syntrophobacteraceae;g__JABUEY01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005377625.1	s__Desulfoglaeba alkanexedens	76.9917	81	1663	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__DSM-9756;g__Desulfoglaeba	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012517535.1	s__JAAYUU01 sp012517535	76.9236	95	1663	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__Syntrophobacteraceae;g__JAAYUU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001603845.1	s__SbD1 sp001603845	76.7527	140	1663	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__Syntrophobacteraceae;g__SbD1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012517315.1	s__JAAYUJ01 sp012517315	76.6086	124	1663	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__Syntrophobacteraceae;g__JAAYUJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007125915.1	s__SLCH01 sp007125915	76.3849	52	1663	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__Syntrophobacteraceae;g__SLCH01	95.0	98.91	98.79	0.74	0.66	4	-
GCA_012517775.1	s__JAAYUJ01 sp012517775	76.3341	70	1663	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__Syntrophobacteraceae;g__JAAYUJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018053185.1	s__JAGPLX01 sp018053185	76.2082	90	1663	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__Syntrophobacteraceae;g__JAGPLX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003566995.1	s__SLCH01 sp003566995	76.1525	74	1663	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__Syntrophobacteraceae;g__SLCH01	95.0	99.54	99.54	0.90	0.90	2	-
GCF_900176285.1	s__Desulfacinum hydrothermale	76.1301	92	1663	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__DSM-9756;g__Desulfacinum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002298995.1	s__SbD1 sp002298995	75.7648	67	1663	d__Bacteria;p__Desulfobacterota;c__Syntrophobacteria;o__Syntrophobacterales;f__Syntrophobacteraceae;g__SbD1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:43:02,247] [INFO] GTDB search result was written to GCF_000014965.1_ASM1496v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:43:02,248] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:43:02,251] [INFO] DFAST_QC result json was written to GCF_000014965.1_ASM1496v1_genomic.fna/dqc_result.json
[2024-01-25 17:43:02,251] [INFO] DFAST_QC completed!
[2024-01-25 17:43:02,251] [INFO] Total running time: 0h1m27s