[2023-06-19 08:40:18,337] [INFO] DFAST_QC pipeline started.
[2023-06-19 08:40:18,339] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 08:40:18,339] [INFO] DQC Reference Directory: /var/lib/cwl/stgb58a0c3c-9bee-40b8-86e6-a36d2aab528a/dqc_reference
[2023-06-19 08:40:19,479] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 08:40:19,480] [INFO] Task started: Prodigal
[2023-06-19 08:40:19,480] [INFO] Running command: gunzip -c /var/lib/cwl/stg24e207d6-39ad-4b20-b8b8-c800e03fb05e/GCA_013813655.1_ASM1381365v1_genomic.fna.gz | prodigal -d GCA_013813655.1_ASM1381365v1_genomic.fna/cds.fna -a GCA_013813655.1_ASM1381365v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 08:40:32,609] [INFO] Task succeeded: Prodigal
[2023-06-19 08:40:32,609] [INFO] Task started: HMMsearch
[2023-06-19 08:40:32,609] [INFO] Running command: hmmsearch --tblout GCA_013813655.1_ASM1381365v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb58a0c3c-9bee-40b8-86e6-a36d2aab528a/dqc_reference/reference_markers.hmm GCA_013813655.1_ASM1381365v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 08:40:32,843] [INFO] Task succeeded: HMMsearch
[2023-06-19 08:40:32,844] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg24e207d6-39ad-4b20-b8b8-c800e03fb05e/GCA_013813655.1_ASM1381365v1_genomic.fna.gz]
[2023-06-19 08:40:32,897] [INFO] Query marker FASTA was written to GCA_013813655.1_ASM1381365v1_genomic.fna/markers.fasta
[2023-06-19 08:40:32,897] [INFO] Task started: Blastn
[2023-06-19 08:40:32,897] [INFO] Running command: blastn -query GCA_013813655.1_ASM1381365v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb58a0c3c-9bee-40b8-86e6-a36d2aab528a/dqc_reference/reference_markers.fasta -out GCA_013813655.1_ASM1381365v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:40:33,516] [INFO] Task succeeded: Blastn
[2023-06-19 08:40:33,519] [INFO] Selected 21 target genomes.
[2023-06-19 08:40:33,519] [INFO] Target genome list was writen to GCA_013813655.1_ASM1381365v1_genomic.fna/target_genomes.txt
[2023-06-19 08:40:33,521] [INFO] Task started: fastANI
[2023-06-19 08:40:33,521] [INFO] Running command: fastANI --query /var/lib/cwl/stg24e207d6-39ad-4b20-b8b8-c800e03fb05e/GCA_013813655.1_ASM1381365v1_genomic.fna.gz --refList GCA_013813655.1_ASM1381365v1_genomic.fna/target_genomes.txt --output GCA_013813655.1_ASM1381365v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 08:40:50,337] [INFO] Task succeeded: fastANI
[2023-06-19 08:40:50,337] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb58a0c3c-9bee-40b8-86e6-a36d2aab528a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 08:40:50,338] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb58a0c3c-9bee-40b8-86e6-a36d2aab528a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 08:40:50,347] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 08:40:50,347] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 08:40:50,347] [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
Lacipirellula parvula	strain=PX69	GCA_009177095.1	2650471	2650471	type	True	78.3678	425	1269	95	below_threshold
Lacipirellula limnantheis	strain=I41	GCA_007746075.1	2528024	2528024	type	True	77.8791	399	1269	95	below_threshold
Pirellulimonas nuda	strain=Pla175	GCA_007750855.1	2528009	2528009	type	True	76.4924	167	1269	95	below_threshold
Pseudobythopirellula maris	strain=Mal64	GCA_007859945.1	2527991	2527991	type	True	76.4622	153	1269	95	below_threshold
Botrimarina mediterranea	strain=Spa11	GCA_007753265.1	2528022	2528022	type	True	76.3735	142	1269	95	below_threshold
Posidoniimonas polymericola	strain=Pla123a	GCA_007859935.1	2528002	2528002	type	True	76.3654	170	1269	95	below_threshold
Posidoniimonas corsicana	strain=KOR34	GCA_007859765.1	1938618	1938618	type	True	76.3651	169	1269	95	below_threshold
Botrimarina colliarenosi	strain=Pla108	GCA_007859955.1	2528001	2528001	type	True	76.2582	152	1269	95	below_threshold
Adhaeretor mobilis	strain=HG15A2	GCA_007741515.1	1930276	1930276	type	True	75.5674	65	1269	95	below_threshold
Tautonia plasticadhaerens	strain=ElP	GCA_007752535.1	2527974	2527974	type	True	75.2293	98	1269	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 08:40:50,350] [INFO] DFAST Taxonomy check result was written to GCA_013813655.1_ASM1381365v1_genomic.fna/tc_result.tsv
[2023-06-19 08:40:50,351] [INFO] ===== Taxonomy check completed =====
[2023-06-19 08:40:50,351] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 08:40:50,351] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb58a0c3c-9bee-40b8-86e6-a36d2aab528a/dqc_reference/checkm_data
[2023-06-19 08:40:50,352] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 08:40:50,409] [INFO] Task started: CheckM
[2023-06-19 08:40:50,409] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013813655.1_ASM1381365v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013813655.1_ASM1381365v1_genomic.fna/checkm_input GCA_013813655.1_ASM1381365v1_genomic.fna/checkm_result
[2023-06-19 08:41:29,592] [INFO] Task succeeded: CheckM
[2023-06-19 08:41:29,593] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.76%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 08:41:29,620] [INFO] ===== Completeness check finished =====
[2023-06-19 08:41:29,620] [INFO] ===== Start GTDB Search =====
[2023-06-19 08:41:29,621] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013813655.1_ASM1381365v1_genomic.fna/markers.fasta)
[2023-06-19 08:41:29,621] [INFO] Task started: Blastn
[2023-06-19 08:41:29,621] [INFO] Running command: blastn -query GCA_013813655.1_ASM1381365v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb58a0c3c-9bee-40b8-86e6-a36d2aab528a/dqc_reference/reference_markers_gtdb.fasta -out GCA_013813655.1_ASM1381365v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:41:30,570] [INFO] Task succeeded: Blastn
[2023-06-19 08:41:30,574] [INFO] Selected 21 target genomes.
[2023-06-19 08:41:30,574] [INFO] Target genome list was writen to GCA_013813655.1_ASM1381365v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 08:41:30,582] [INFO] Task started: fastANI
[2023-06-19 08:41:30,583] [INFO] Running command: fastANI --query /var/lib/cwl/stg24e207d6-39ad-4b20-b8b8-c800e03fb05e/GCA_013813655.1_ASM1381365v1_genomic.fna.gz --refList GCA_013813655.1_ASM1381365v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013813655.1_ASM1381365v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 08:41:48,720] [INFO] Task succeeded: fastANI
[2023-06-19 08:41:48,732] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-19 08:41:48,733] [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_009177095.1	s__Lacipirellula parvula	78.3865	423	1269	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Lacipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013822725.1	s__Lacipirellula sp013822725	78.2545	377	1269	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Lacipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007746075.1	s__Lacipirellula limnantheis	77.9198	394	1269	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Lacipirellula	95.0	97.19	97.19	0.90	0.90	2	-
GCA_003576855.1	s__Lacipirellula sp003576855	77.7132	339	1269	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Lacipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002702655.1	s__GCA-2702655 sp002702655	77.0466	242	1269	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__GCA-2702655	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007745835.1	s__Botrimarina sp007745835	76.6272	137	1269	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Botrimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007750855.1	s__Pirellulimonas nuda	76.4776	167	1269	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Pirellulimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859935.1	s__Posidoniimonas polymericola	76.3868	168	1269	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Posidoniimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003389325.1	s__LB-PLM-3 sp003389325	76.2217	106	1269	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__PALSA-1355;g__LB-PLM-3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464525.1	s__Ga0077529 sp001464525	75.8272	91	1269	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Ga0077529	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018242585.1	s__JAFEBQ01 sp018242585	75.8037	84	1269	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__PNKZ01;g__JAFEBQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007741515.1	s__HG15A2 sp007741515	75.5674	65	1269	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__HG15A2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013152205.1	s__Bythopirellula sp013152205	75.5535	59	1269	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Bythopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793185.1	s__JAEUIK01 sp016793185	75.3648	67	1269	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__JAEUIK01;g__JAEUIK01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 08:41:48,737] [INFO] GTDB search result was written to GCA_013813655.1_ASM1381365v1_genomic.fna/result_gtdb.tsv
[2023-06-19 08:41:48,737] [INFO] ===== GTDB Search completed =====
[2023-06-19 08:41:48,742] [INFO] DFAST_QC result json was written to GCA_013813655.1_ASM1381365v1_genomic.fna/dqc_result.json
[2023-06-19 08:41:48,742] [INFO] DFAST_QC completed!
[2023-06-19 08:41:48,742] [INFO] Total running time: 0h1m30s