[2023-06-18 21:50:41,179] [INFO] DFAST_QC pipeline started.
[2023-06-18 21:50:41,200] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 21:50:41,201] [INFO] DQC Reference Directory: /var/lib/cwl/stg2a5f12c6-a94f-4b99-9aae-b228d214b20a/dqc_reference
[2023-06-18 21:50:43,299] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 21:50:43,300] [INFO] Task started: Prodigal
[2023-06-18 21:50:43,300] [INFO] Running command: gunzip -c /var/lib/cwl/stg24b6efb5-a54d-4412-9bc3-57b8c4c97c43/GCA_018665445.1_ASM1866544v1_genomic.fna.gz | prodigal -d GCA_018665445.1_ASM1866544v1_genomic.fna/cds.fna -a GCA_018665445.1_ASM1866544v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 21:50:44,763] [INFO] Task succeeded: Prodigal
[2023-06-18 21:50:44,763] [INFO] Task started: HMMsearch
[2023-06-18 21:50:44,763] [INFO] Running command: hmmsearch --tblout GCA_018665445.1_ASM1866544v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2a5f12c6-a94f-4b99-9aae-b228d214b20a/dqc_reference/reference_markers.hmm GCA_018665445.1_ASM1866544v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 21:50:45,038] [INFO] Task succeeded: HMMsearch
[2023-06-18 21:50:45,040] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg24b6efb5-a54d-4412-9bc3-57b8c4c97c43/GCA_018665445.1_ASM1866544v1_genomic.fna.gz]
[2023-06-18 21:50:45,101] [INFO] Query marker FASTA was written to GCA_018665445.1_ASM1866544v1_genomic.fna/markers.fasta
[2023-06-18 21:50:45,102] [INFO] Task started: Blastn
[2023-06-18 21:50:45,102] [INFO] Running command: blastn -query GCA_018665445.1_ASM1866544v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a5f12c6-a94f-4b99-9aae-b228d214b20a/dqc_reference/reference_markers.fasta -out GCA_018665445.1_ASM1866544v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 21:50:47,783] [INFO] Task succeeded: Blastn
[2023-06-18 21:50:47,788] [INFO] Selected 15 target genomes.
[2023-06-18 21:50:47,788] [INFO] Target genome list was writen to GCA_018665445.1_ASM1866544v1_genomic.fna/target_genomes.txt
[2023-06-18 21:50:47,791] [INFO] Task started: fastANI
[2023-06-18 21:50:47,791] [INFO] Running command: fastANI --query /var/lib/cwl/stg24b6efb5-a54d-4412-9bc3-57b8c4c97c43/GCA_018665445.1_ASM1866544v1_genomic.fna.gz --refList GCA_018665445.1_ASM1866544v1_genomic.fna/target_genomes.txt --output GCA_018665445.1_ASM1866544v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 21:50:54,782] [INFO] Task succeeded: fastANI
[2023-06-18 21:50:54,783] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2a5f12c6-a94f-4b99-9aae-b228d214b20a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 21:50:54,783] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2a5f12c6-a94f-4b99-9aae-b228d214b20a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 21:50:54,786] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 21:50:54,786] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 21:50:54,786] [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
--------------------------------------------------------------------------------
[2023-06-18 21:50:54,789] [INFO] DFAST Taxonomy check result was written to GCA_018665445.1_ASM1866544v1_genomic.fna/tc_result.tsv
[2023-06-18 21:50:54,792] [INFO] ===== Taxonomy check completed =====
[2023-06-18 21:50:54,793] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 21:50:54,793] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2a5f12c6-a94f-4b99-9aae-b228d214b20a/dqc_reference/checkm_data
[2023-06-18 21:50:54,797] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 21:50:54,814] [INFO] Task started: CheckM
[2023-06-18 21:50:54,815] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018665445.1_ASM1866544v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018665445.1_ASM1866544v1_genomic.fna/checkm_input GCA_018665445.1_ASM1866544v1_genomic.fna/checkm_result
[2023-06-18 21:51:07,771] [INFO] Task succeeded: CheckM
[2023-06-18 21:51:07,772] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 21:51:07,797] [INFO] ===== Completeness check finished =====
[2023-06-18 21:51:07,797] [INFO] ===== Start GTDB Search =====
[2023-06-18 21:51:07,797] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018665445.1_ASM1866544v1_genomic.fna/markers.fasta)
[2023-06-18 21:51:07,798] [INFO] Task started: Blastn
[2023-06-18 21:51:07,798] [INFO] Running command: blastn -query GCA_018665445.1_ASM1866544v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a5f12c6-a94f-4b99-9aae-b228d214b20a/dqc_reference/reference_markers_gtdb.fasta -out GCA_018665445.1_ASM1866544v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 21:51:08,610] [INFO] Task succeeded: Blastn
[2023-06-18 21:51:08,615] [INFO] Selected 8 target genomes.
[2023-06-18 21:51:08,615] [INFO] Target genome list was writen to GCA_018665445.1_ASM1866544v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 21:51:08,620] [INFO] Task started: fastANI
[2023-06-18 21:51:08,620] [INFO] Running command: fastANI --query /var/lib/cwl/stg24b6efb5-a54d-4412-9bc3-57b8c4c97c43/GCA_018665445.1_ASM1866544v1_genomic.fna.gz --refList GCA_018665445.1_ASM1866544v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018665445.1_ASM1866544v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 21:51:10,100] [INFO] Task succeeded: fastANI
[2023-06-18 21:51:10,114] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 21:51:10,114] [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_000402755.1	s__Marinisoma sp000402755	95.3254	218	274	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	95.42	95.16	0.79	0.76	17	conclusive
GCA_905182795.1	s__Marinisoma sp905182795	90.164	243	274	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014240005.1	s__Marinisoma sp014240005	86.6123	197	274	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	96.63	96.63	0.87	0.87	2	-
GCA_002701645.1	s__Marinisoma sp002701645	86.3757	174	274	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000402815.1	s__Marinisoma atlanticum	84.0707	219	274	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	99.54	99.22	0.95	0.89	4	-
GCA_902624275.1	s__Marinisoma sp902624275	77.5977	73	274	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000402655.1	s__Marinisoma sp000402655	77.5579	78	274	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	96.42	95.83	0.93	0.92	4	-
GCA_902578385.1	s__Marinisoma sp002710515	77.4931	78	274	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	97.88	96.56	0.86	0.83	7	-
--------------------------------------------------------------------------------
[2023-06-18 21:51:10,116] [INFO] GTDB search result was written to GCA_018665445.1_ASM1866544v1_genomic.fna/result_gtdb.tsv
[2023-06-18 21:51:10,117] [INFO] ===== GTDB Search completed =====
[2023-06-18 21:51:10,120] [INFO] DFAST_QC result json was written to GCA_018665445.1_ASM1866544v1_genomic.fna/dqc_result.json
[2023-06-18 21:51:10,120] [INFO] DFAST_QC completed!
[2023-06-18 21:51:10,120] [INFO] Total running time: 0h0m29s