[2023-06-26 23:22:09,348] [INFO] DFAST_QC pipeline started.
[2023-06-26 23:22:09,365] [INFO] DFAST_QC version: 0.5.7
[2023-06-26 23:22:09,366] [INFO] DQC Reference Directory: /var/lib/cwl/stg6f2f6723-a0f5-47af-bf1f-86ef20e57963/dqc_reference
[2023-06-26 23:22:11,371] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-26 23:22:11,373] [INFO] Task started: Prodigal
[2023-06-26 23:22:11,373] [INFO] Running command: gunzip -c /var/lib/cwl/stg30701e33-28a7-4108-8e29-9d12060e8025/GCA_026645935.1_ASM2664593v1_genomic.fna.gz | prodigal -d GCA_026645935.1_ASM2664593v1_genomic.fna/cds.fna -a GCA_026645935.1_ASM2664593v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-26 23:22:24,566] [INFO] Task succeeded: Prodigal
[2023-06-26 23:22:24,566] [INFO] Task started: HMMsearch
[2023-06-26 23:22:24,566] [INFO] Running command: hmmsearch --tblout GCA_026645935.1_ASM2664593v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6f2f6723-a0f5-47af-bf1f-86ef20e57963/dqc_reference/reference_markers.hmm GCA_026645935.1_ASM2664593v1_genomic.fna/protein.faa > /dev/null
[2023-06-26 23:22:24,917] [INFO] Task succeeded: HMMsearch
[2023-06-26 23:22:24,918] [INFO] Found 6/6 markers.
[2023-06-26 23:22:24,971] [INFO] Query marker FASTA was written to GCA_026645935.1_ASM2664593v1_genomic.fna/markers.fasta
[2023-06-26 23:22:24,972] [INFO] Task started: Blastn
[2023-06-26 23:22:24,972] [INFO] Running command: blastn -query GCA_026645935.1_ASM2664593v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f2f6723-a0f5-47af-bf1f-86ef20e57963/dqc_reference/reference_markers.fasta -out GCA_026645935.1_ASM2664593v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 23:22:25,614] [INFO] Task succeeded: Blastn
[2023-06-26 23:22:25,620] [INFO] Selected 22 target genomes.
[2023-06-26 23:22:25,621] [INFO] Target genome list was writen to GCA_026645935.1_ASM2664593v1_genomic.fna/target_genomes.txt
[2023-06-26 23:22:25,625] [INFO] Task started: fastANI
[2023-06-26 23:22:25,626] [INFO] Running command: fastANI --query /var/lib/cwl/stg30701e33-28a7-4108-8e29-9d12060e8025/GCA_026645935.1_ASM2664593v1_genomic.fna.gz --refList GCA_026645935.1_ASM2664593v1_genomic.fna/target_genomes.txt --output GCA_026645935.1_ASM2664593v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-26 23:22:39,517] [INFO] Task succeeded: fastANI
[2023-06-26 23:22:39,518] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6f2f6723-a0f5-47af-bf1f-86ef20e57963/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-26 23:22:39,518] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6f2f6723-a0f5-47af-bf1f-86ef20e57963/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-26 23:22:39,520] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-26 23:22:39,520] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-26 23:22:39,520] [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
--------------------------------------------------------------------------------
[2023-06-26 23:22:39,524] [INFO] DFAST Taxonomy check result was written to GCA_026645935.1_ASM2664593v1_genomic.fna/tc_result.tsv
[2023-06-26 23:22:39,525] [INFO] ===== Taxonomy check completed =====
[2023-06-26 23:22:39,526] [INFO] ===== Start completeness check using CheckM =====
[2023-06-26 23:22:39,526] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6f2f6723-a0f5-47af-bf1f-86ef20e57963/dqc_reference/checkm_data
[2023-06-26 23:22:39,529] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-26 23:22:39,580] [INFO] Task started: CheckM
[2023-06-26 23:22:39,581] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026645935.1_ASM2664593v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026645935.1_ASM2664593v1_genomic.fna/checkm_input GCA_026645935.1_ASM2664593v1_genomic.fna/checkm_result
[2023-06-26 23:23:21,806] [INFO] Task succeeded: CheckM
[2023-06-26 23:23:21,808] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-26 23:23:21,836] [INFO] ===== Completeness check finished =====
[2023-06-26 23:23:21,837] [INFO] ===== Start GTDB Search =====
[2023-06-26 23:23:21,837] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026645935.1_ASM2664593v1_genomic.fna/markers.fasta)
[2023-06-26 23:23:21,838] [INFO] Task started: Blastn
[2023-06-26 23:23:21,838] [INFO] Running command: blastn -query GCA_026645935.1_ASM2664593v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f2f6723-a0f5-47af-bf1f-86ef20e57963/dqc_reference/reference_markers_gtdb.fasta -out GCA_026645935.1_ASM2664593v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 23:23:22,757] [INFO] Task succeeded: Blastn
[2023-06-26 23:23:22,782] [INFO] Selected 18 target genomes.
[2023-06-26 23:23:22,782] [INFO] Target genome list was writen to GCA_026645935.1_ASM2664593v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-26 23:23:22,792] [INFO] Task started: fastANI
[2023-06-26 23:23:22,793] [INFO] Running command: fastANI --query /var/lib/cwl/stg30701e33-28a7-4108-8e29-9d12060e8025/GCA_026645935.1_ASM2664593v1_genomic.fna.gz --refList GCA_026645935.1_ASM2664593v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026645935.1_ASM2664593v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-26 23:23:37,015] [INFO] Task succeeded: fastANI
[2023-06-26 23:23:37,034] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-26 23:23:37,034] [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
GCA_015075725.1	s__OLB14 sp008363285	94.0878	1244	1409	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__OLB14	95.0	98.20	98.20	0.92	0.92	2	-
GCA_016703605.1	s__OLB14 sp016703605	80.8254	770	1409	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__OLB14	95.0	98.59	98.59	0.83	0.83	2	-
GCA_900696595.1	s__OLB14 sp900696595	79.8031	577	1409	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__OLB14	95.0	98.68	97.00	0.88	0.84	4	-
GCA_016191955.1	s__OLB14 sp016191955	79.376	578	1409	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__OLB14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013112685.1	s__OLB14 sp013112685	79.3738	590	1409	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__OLB14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016721315.1	s__OLB14 sp016721315	78.9203	517	1409	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__OLB14	95.0	98.70	98.69	0.90	0.88	3	-
GCA_017303735.1	s__OLB14 sp017303735	78.7973	481	1409	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__OLB14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013388795.1	s__OLB14 sp013388795	78.7716	398	1409	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__OLB14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017303655.1	s__OLB14 sp017303655	78.7322	465	1409	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__OLB14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016875755.1	s__OLB14 sp016875755	78.6847	301	1409	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__OLB14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013360875.1	s__UBA12294 sp013360875	78.3919	292	1409	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA12294	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014860745.1	s__OLB14 sp014860745	78.2693	420	1409	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__OLB14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016235445.1	s__OLB14 sp016235445	77.7573	398	1409	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__OLB14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016714565.1	s__OLB14 sp016714565	77.6667	343	1409	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__OLB14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014860805.1	s__OLB14 sp014860805	77.6405	306	1409	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__OLB14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016191985.1	s__OLB14 sp016191985	77.2701	289	1409	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__OLB14	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-26 23:23:37,037] [INFO] GTDB search result was written to GCA_026645935.1_ASM2664593v1_genomic.fna/result_gtdb.tsv
[2023-06-26 23:23:37,038] [INFO] ===== GTDB Search completed =====
[2023-06-26 23:23:37,041] [INFO] DFAST_QC result json was written to GCA_026645935.1_ASM2664593v1_genomic.fna/dqc_result.json
[2023-06-26 23:23:37,042] [INFO] DFAST_QC completed!
[2023-06-26 23:23:37,042] [INFO] Total running time: 0h1m28s