[2023-06-08 12:08:20,855] [INFO] DFAST_QC pipeline started.
[2023-06-08 12:08:20,886] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 12:08:20,886] [INFO] DQC Reference Directory: /var/lib/cwl/stg002a65fe-9c1a-45ab-8319-8d16f7834d8a/dqc_reference
[2023-06-08 12:08:23,095] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 12:08:23,096] [INFO] Task started: Prodigal
[2023-06-08 12:08:23,097] [INFO] Running command: gunzip -c /var/lib/cwl/stga14da11e-a3ac-40c9-ab63-1609a18815d7/GCA_902751565.1_P1994_106_bin40_mag_fasta_genomic.fna.gz | prodigal -d GCA_902751565.1_P1994_106_bin40_mag_fasta_genomic.fna/cds.fna -a GCA_902751565.1_P1994_106_bin40_mag_fasta_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 12:08:28,374] [INFO] Task succeeded: Prodigal
[2023-06-08 12:08:28,374] [INFO] Task started: HMMsearch
[2023-06-08 12:08:28,374] [INFO] Running command: hmmsearch --tblout GCA_902751565.1_P1994_106_bin40_mag_fasta_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg002a65fe-9c1a-45ab-8319-8d16f7834d8a/dqc_reference/reference_markers.hmm GCA_902751565.1_P1994_106_bin40_mag_fasta_genomic.fna/protein.faa > /dev/null
[2023-06-08 12:08:28,587] [INFO] Task succeeded: HMMsearch
[2023-06-08 12:08:28,589] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga14da11e-a3ac-40c9-ab63-1609a18815d7/GCA_902751565.1_P1994_106_bin40_mag_fasta_genomic.fna.gz]
[2023-06-08 12:08:28,618] [INFO] Query marker FASTA was written to GCA_902751565.1_P1994_106_bin40_mag_fasta_genomic.fna/markers.fasta
[2023-06-08 12:08:28,618] [INFO] Task started: Blastn
[2023-06-08 12:08:28,618] [INFO] Running command: blastn -query GCA_902751565.1_P1994_106_bin40_mag_fasta_genomic.fna/markers.fasta -db /var/lib/cwl/stg002a65fe-9c1a-45ab-8319-8d16f7834d8a/dqc_reference/reference_markers.fasta -out GCA_902751565.1_P1994_106_bin40_mag_fasta_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:08:29,333] [INFO] Task succeeded: Blastn
[2023-06-08 12:08:29,338] [INFO] Selected 28 target genomes.
[2023-06-08 12:08:29,338] [INFO] Target genome list was writen to GCA_902751565.1_P1994_106_bin40_mag_fasta_genomic.fna/target_genomes.txt
[2023-06-08 12:08:29,342] [INFO] Task started: fastANI
[2023-06-08 12:08:29,342] [INFO] Running command: fastANI --query /var/lib/cwl/stga14da11e-a3ac-40c9-ab63-1609a18815d7/GCA_902751565.1_P1994_106_bin40_mag_fasta_genomic.fna.gz --refList GCA_902751565.1_P1994_106_bin40_mag_fasta_genomic.fna/target_genomes.txt --output GCA_902751565.1_P1994_106_bin40_mag_fasta_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 12:08:49,515] [INFO] Task succeeded: fastANI
[2023-06-08 12:08:49,515] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg002a65fe-9c1a-45ab-8319-8d16f7834d8a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 12:08:49,516] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg002a65fe-9c1a-45ab-8319-8d16f7834d8a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 12:08:49,531] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 12:08:49,531] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 12:08:49,531] [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
Skermanella mucosa	strain=KEMB 2255-438	GCA_016765655.2	1789672	1789672	type	True	76.0478	51	405	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	75.8813	51	405	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	75.8645	51	405	95	below_threshold
Aliidongia dinghuensis	strain=CGMCC 1.15725	GCA_014643535.1	1867774	1867774	type	True	75.8497	50	405	95	below_threshold
Azospirillum griseum	strain=L-25-5 w-1	GCA_003966125.1	2496639	2496639	type	True	75.7746	56	405	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	75.6114	51	405	95	below_threshold
Caenispirillum salinarum	strain=AK4	GCA_000315795.1	859058	859058	type	True	75.461	52	405	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 12:08:49,534] [INFO] DFAST Taxonomy check result was written to GCA_902751565.1_P1994_106_bin40_mag_fasta_genomic.fna/tc_result.tsv
[2023-06-08 12:08:49,535] [INFO] ===== Taxonomy check completed =====
[2023-06-08 12:08:49,535] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 12:08:49,535] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg002a65fe-9c1a-45ab-8319-8d16f7834d8a/dqc_reference/checkm_data
[2023-06-08 12:08:49,537] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 12:08:49,566] [INFO] Task started: CheckM
[2023-06-08 12:08:49,566] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902751565.1_P1994_106_bin40_mag_fasta_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902751565.1_P1994_106_bin40_mag_fasta_genomic.fna/checkm_input GCA_902751565.1_P1994_106_bin40_mag_fasta_genomic.fna/checkm_result
[2023-06-08 12:09:11,163] [INFO] Task succeeded: CheckM
[2023-06-08 12:09:11,164] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 12:09:11,188] [INFO] ===== Completeness check finished =====
[2023-06-08 12:09:11,189] [INFO] ===== Start GTDB Search =====
[2023-06-08 12:09:11,190] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902751565.1_P1994_106_bin40_mag_fasta_genomic.fna/markers.fasta)
[2023-06-08 12:09:11,190] [INFO] Task started: Blastn
[2023-06-08 12:09:11,190] [INFO] Running command: blastn -query GCA_902751565.1_P1994_106_bin40_mag_fasta_genomic.fna/markers.fasta -db /var/lib/cwl/stg002a65fe-9c1a-45ab-8319-8d16f7834d8a/dqc_reference/reference_markers_gtdb.fasta -out GCA_902751565.1_P1994_106_bin40_mag_fasta_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:09:12,367] [INFO] Task succeeded: Blastn
[2023-06-08 12:09:12,371] [INFO] Selected 25 target genomes.
[2023-06-08 12:09:12,371] [INFO] Target genome list was writen to GCA_902751565.1_P1994_106_bin40_mag_fasta_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 12:09:12,419] [INFO] Task started: fastANI
[2023-06-08 12:09:12,420] [INFO] Running command: fastANI --query /var/lib/cwl/stga14da11e-a3ac-40c9-ab63-1609a18815d7/GCA_902751565.1_P1994_106_bin40_mag_fasta_genomic.fna.gz --refList GCA_902751565.1_P1994_106_bin40_mag_fasta_genomic.fna/target_genomes_gtdb.txt --output GCA_902751565.1_P1994_106_bin40_mag_fasta_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 12:09:28,460] [INFO] Task succeeded: fastANI
[2023-06-08 12:09:28,469] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 12:09:28,469] [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_009380075.1	s__WHSO01 sp009380075	78.2969	220	405	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SMXQ01;f__SMXQ01;g__WHSO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004356985.1	s__SMXQ01 sp004356985	77.1235	111	405	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SMXQ01;f__SMXQ01;g__SMXQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006980715.1	s__Oleiliquidispirillum nitrogeniifigens	76.5369	56	405	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Oleiliquidispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008039615.1	s__SYSU-D60007 sp008039615	75.8645	51	405	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__SYSU-D60007	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 12:09:28,471] [INFO] GTDB search result was written to GCA_902751565.1_P1994_106_bin40_mag_fasta_genomic.fna/result_gtdb.tsv
[2023-06-08 12:09:28,472] [INFO] ===== GTDB Search completed =====
[2023-06-08 12:09:28,475] [INFO] DFAST_QC result json was written to GCA_902751565.1_P1994_106_bin40_mag_fasta_genomic.fna/dqc_result.json
[2023-06-08 12:09:28,475] [INFO] DFAST_QC completed!
[2023-06-08 12:09:28,475] [INFO] Total running time: 0h1m8s