[2023-06-19 10:56:19,975] [INFO] DFAST_QC pipeline started.
[2023-06-19 10:56:19,978] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 10:56:19,978] [INFO] DQC Reference Directory: /var/lib/cwl/stg21b29555-4740-4f13-bdb9-35f00467bc70/dqc_reference
[2023-06-19 10:56:21,242] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 10:56:21,244] [INFO] Task started: Prodigal
[2023-06-19 10:56:21,244] [INFO] Running command: gunzip -c /var/lib/cwl/stg6a0a2e8f-8bda-44dd-afb2-3e623ca90992/GCA_013202385.1_ASM1320238v1_genomic.fna.gz | prodigal -d GCA_013202385.1_ASM1320238v1_genomic.fna/cds.fna -a GCA_013202385.1_ASM1320238v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 10:56:28,040] [INFO] Task succeeded: Prodigal
[2023-06-19 10:56:28,040] [INFO] Task started: HMMsearch
[2023-06-19 10:56:28,040] [INFO] Running command: hmmsearch --tblout GCA_013202385.1_ASM1320238v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg21b29555-4740-4f13-bdb9-35f00467bc70/dqc_reference/reference_markers.hmm GCA_013202385.1_ASM1320238v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 10:56:28,280] [INFO] Task succeeded: HMMsearch
[2023-06-19 10:56:28,281] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg6a0a2e8f-8bda-44dd-afb2-3e623ca90992/GCA_013202385.1_ASM1320238v1_genomic.fna.gz]
[2023-06-19 10:56:28,311] [INFO] Query marker FASTA was written to GCA_013202385.1_ASM1320238v1_genomic.fna/markers.fasta
[2023-06-19 10:56:28,312] [INFO] Task started: Blastn
[2023-06-19 10:56:28,312] [INFO] Running command: blastn -query GCA_013202385.1_ASM1320238v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg21b29555-4740-4f13-bdb9-35f00467bc70/dqc_reference/reference_markers.fasta -out GCA_013202385.1_ASM1320238v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 10:56:28,802] [INFO] Task succeeded: Blastn
[2023-06-19 10:56:28,805] [INFO] Selected 4 target genomes.
[2023-06-19 10:56:28,805] [INFO] Target genome list was writen to GCA_013202385.1_ASM1320238v1_genomic.fna/target_genomes.txt
[2023-06-19 10:56:28,807] [INFO] Task started: fastANI
[2023-06-19 10:56:28,807] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a0a2e8f-8bda-44dd-afb2-3e623ca90992/GCA_013202385.1_ASM1320238v1_genomic.fna.gz --refList GCA_013202385.1_ASM1320238v1_genomic.fna/target_genomes.txt --output GCA_013202385.1_ASM1320238v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 10:56:30,792] [INFO] Task succeeded: fastANI
[2023-06-19 10:56:30,792] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg21b29555-4740-4f13-bdb9-35f00467bc70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 10:56:30,793] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg21b29555-4740-4f13-bdb9-35f00467bc70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 10:56:30,795] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 10:56:30,795] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 10:56:30,795] [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
--------------------------------------------------------------------------------
[2023-06-19 10:56:30,798] [INFO] DFAST Taxonomy check result was written to GCA_013202385.1_ASM1320238v1_genomic.fna/tc_result.tsv
[2023-06-19 10:56:30,799] [INFO] ===== Taxonomy check completed =====
[2023-06-19 10:56:30,799] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 10:56:30,799] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg21b29555-4740-4f13-bdb9-35f00467bc70/dqc_reference/checkm_data
[2023-06-19 10:56:30,803] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 10:56:30,838] [INFO] Task started: CheckM
[2023-06-19 10:56:30,839] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013202385.1_ASM1320238v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013202385.1_ASM1320238v1_genomic.fna/checkm_input GCA_013202385.1_ASM1320238v1_genomic.fna/checkm_result
[2023-06-19 10:56:58,398] [INFO] Task succeeded: CheckM
[2023-06-19 10:56:58,400] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 29.63%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-19 10:56:58,424] [INFO] ===== Completeness check finished =====
[2023-06-19 10:56:58,424] [INFO] ===== Start GTDB Search =====
[2023-06-19 10:56:58,424] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013202385.1_ASM1320238v1_genomic.fna/markers.fasta)
[2023-06-19 10:56:58,425] [INFO] Task started: Blastn
[2023-06-19 10:56:58,425] [INFO] Running command: blastn -query GCA_013202385.1_ASM1320238v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg21b29555-4740-4f13-bdb9-35f00467bc70/dqc_reference/reference_markers_gtdb.fasta -out GCA_013202385.1_ASM1320238v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 10:56:58,862] [INFO] Task succeeded: Blastn
[2023-06-19 10:56:58,865] [INFO] Selected 7 target genomes.
[2023-06-19 10:56:58,866] [INFO] Target genome list was writen to GCA_013202385.1_ASM1320238v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 10:56:58,870] [INFO] Task started: fastANI
[2023-06-19 10:56:58,870] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a0a2e8f-8bda-44dd-afb2-3e623ca90992/GCA_013202385.1_ASM1320238v1_genomic.fna.gz --refList GCA_013202385.1_ASM1320238v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013202385.1_ASM1320238v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 10:57:02,980] [INFO] Task succeeded: fastANI
[2023-06-19 10:57:02,987] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 10:57:02,987] [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_013202385.1	s__JABMPR01 sp013202385	100.0	880	898	d__Bacteria;p__Marinisomatota;c__UBA8477;o__UBA8477;f__UBA8477;g__JABMPR01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016784545.1	s__JABMPR01 sp016784545	76.7688	117	898	d__Bacteria;p__Marinisomatota;c__UBA8477;o__UBA8477;f__UBA8477;g__JABMPR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016844955.1	s__JABMPR01 sp016844955	76.5258	104	898	d__Bacteria;p__Marinisomatota;c__UBA8477;o__UBA8477;f__UBA8477;g__JABMPR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018673925.1	s__JABMPR01 sp018673925	76.3913	110	898	d__Bacteria;p__Marinisomatota;c__UBA8477;o__UBA8477;f__UBA8477;g__JABMPR01	95.0	99.95	99.91	0.96	0.94	16	-
GCA_016844945.1	s__JABMPR01 sp016844945	76.3102	97	898	d__Bacteria;p__Marinisomatota;c__UBA8477;o__UBA8477;f__UBA8477;g__JABMPR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018650445.1	s__JABMPR01 sp018650445	76.2357	112	898	d__Bacteria;p__Marinisomatota;c__UBA8477;o__UBA8477;f__UBA8477;g__JABMPR01	95.0	99.76	99.61	0.86	0.82	5	-
--------------------------------------------------------------------------------
[2023-06-19 10:57:02,989] [INFO] GTDB search result was written to GCA_013202385.1_ASM1320238v1_genomic.fna/result_gtdb.tsv
[2023-06-19 10:57:02,989] [INFO] ===== GTDB Search completed =====
[2023-06-19 10:57:02,992] [INFO] DFAST_QC result json was written to GCA_013202385.1_ASM1320238v1_genomic.fna/dqc_result.json
[2023-06-19 10:57:02,992] [INFO] DFAST_QC completed!
[2023-06-19 10:57:02,992] [INFO] Total running time: 0h0m43s