[2023-03-18 20:59:43,925] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:59:43,925] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:59:43,925] [INFO] DQC Reference Directory: /var/lib/cwl/stgabdf93b0-cd94-48ca-b74c-c83f62283d94/dqc_reference
[2023-03-18 20:59:45,685] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:59:45,685] [INFO] Task started: Prodigal
[2023-03-18 20:59:45,685] [INFO] Running command: cat /var/lib/cwl/stg982bea73-ca27-4919-b851-dafe40f369f2/OceanDNA-b36164.fa | prodigal -d OceanDNA-b36164/cds.fna -a OceanDNA-b36164/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:00:05,842] [INFO] Task succeeded: Prodigal
[2023-03-18 21:00:05,843] [INFO] Task started: HMMsearch
[2023-03-18 21:00:05,843] [INFO] Running command: hmmsearch --tblout OceanDNA-b36164/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgabdf93b0-cd94-48ca-b74c-c83f62283d94/dqc_reference/reference_markers.hmm OceanDNA-b36164/protein.faa > /dev/null
[2023-03-18 21:00:06,074] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:00:06,074] [INFO] Found 6/6 markers.
[2023-03-18 21:00:06,096] [INFO] Query marker FASTA was written to OceanDNA-b36164/markers.fasta
[2023-03-18 21:00:06,097] [INFO] Task started: Blastn
[2023-03-18 21:00:06,097] [INFO] Running command: blastn -query OceanDNA-b36164/markers.fasta -db /var/lib/cwl/stgabdf93b0-cd94-48ca-b74c-c83f62283d94/dqc_reference/reference_markers.fasta -out OceanDNA-b36164/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:00:06,867] [INFO] Task succeeded: Blastn
[2023-03-18 21:00:06,868] [INFO] Selected 24 target genomes.
[2023-03-18 21:00:06,868] [INFO] Target genome list was writen to OceanDNA-b36164/target_genomes.txt
[2023-03-18 21:00:06,896] [INFO] Task started: fastANI
[2023-03-18 21:00:06,896] [INFO] Running command: fastANI --query /var/lib/cwl/stg982bea73-ca27-4919-b851-dafe40f369f2/OceanDNA-b36164.fa --refList OceanDNA-b36164/target_genomes.txt --output OceanDNA-b36164/fastani_result.tsv --threads 1
[2023-03-18 21:00:22,838] [INFO] Task succeeded: fastANI
[2023-03-18 21:00:22,839] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgabdf93b0-cd94-48ca-b74c-c83f62283d94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:00:22,839] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgabdf93b0-cd94-48ca-b74c-c83f62283d94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:00:22,852] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:00:22,852] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 21:00:22,852] [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
Salinisphaera shabanensis	strain=E1L3A	GCA_000215955.3	180542	180542	type	True	84.0005	807	1095	95	below_threshold
Salinisphaera orenii	strain=MK-B5	GCA_003788635.1	856731	856731	type	True	79.9725	587	1095	95	below_threshold
Salinisphaera halophila	strain=YIM 95161	GCA_003732545.1	1304158	1304158	type	True	79.9656	573	1095	95	below_threshold
Salinisphaera japonica	strain=YTM-1	GCA_003788585.1	1304270	1304270	type	True	78.0572	352	1095	95	below_threshold
Xanthomonas citri	strain=LMG867	GCA_020011255.1	346	346	pathovar	True	76.0414	78	1095	95	below_threshold
Xanthomonas citri	strain=CFBP7112	GCA_002218265.1	346	346	pathovar	True	75.9091	82	1095	95	below_threshold
Xanthomonas citri	strain=LMG872	GCA_020011215.1	346	346	pathovar	True	75.8569	75	1095	95	below_threshold
Sulfurivermis fontis	strain=JG42	GCA_004001245.1	1972068	1972068	type	True	75.7784	76	1095	95	below_threshold
Xanthomonas hydrangeae	strain=LMG 31884	GCA_905142475.1	2775159	2775159	type	True	75.7527	83	1095	95	below_threshold
Xanthomonas citri	strain=WHRI 5232	GCA_003064125.1	346	346	pathovar	True	75.7355	82	1095	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_021602465.1	2740517	2740517	suspected-type	True	75.6292	67	1095	95	below_threshold
Vulcaniibacterium gelatinicum	strain=R-5-52-3	GCA_008033445.1	2598725	2598725	type	True	75.6137	86	1095	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_013373915.1	2740517	2740517	suspected-type	True	75.5966	69	1095	95	below_threshold
Solimonas marina	strain=C16B3	GCA_012241385.1	2714601	2714601	type	True	75.5919	104	1095	95	below_threshold
Lysobacter silvisoli	strain=zong2l5	GCA_003382365.1	2293254	2293254	type	True	75.5776	117	1095	95	below_threshold
Thauera chlorobenzoica	strain=3CB-1	GCA_900108255.1	96773	96773	type	True	75.569	79	1095	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	75.5651	86	1095	95	below_threshold
Natronocella acetinitrilica	strain=ANL 6-2	GCA_024170285.1	414046	414046	type	True	75.5456	57	1095	95	below_threshold
Luteimonas marina	strain=FR1330	GCA_007859325.1	488485	488485	type	True	75.469	110	1095	95	below_threshold
Thauera aromatica	strain=K172	GCA_003030465.1	59405	59405	type	True	75.4386	87	1095	95	below_threshold
Azotobacter chroococcum subsp. isscasi	strain=P205	GCA_004327895.1	2528971	353	type	True	75.3907	107	1095	95	below_threshold
Plasticicumulans acidivorans	strain=DSM 23606	GCA_003182095.1	886464	886464	type	True	75.2915	92	1095	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 21:00:22,892] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36164/tc_result.tsv
[2023-03-18 21:00:22,892] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:00:22,893] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:00:22,893] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgabdf93b0-cd94-48ca-b74c-c83f62283d94/dqc_reference/checkm_data
[2023-03-18 21:00:22,894] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:00:22,903] [INFO] Task started: CheckM
[2023-03-18 21:00:22,903] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36164/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36164/checkm_input OceanDNA-b36164/checkm_result
[2023-03-18 21:01:13,810] [INFO] Task succeeded: CheckM
[2023-03-18 21:01:13,810] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 21:01:13,841] [INFO] ===== Completeness check finished =====
[2023-03-18 21:01:13,841] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:01:13,842] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36164/markers.fasta)
[2023-03-18 21:01:13,842] [INFO] Task started: Blastn
[2023-03-18 21:01:13,842] [INFO] Running command: blastn -query OceanDNA-b36164/markers.fasta -db /var/lib/cwl/stgabdf93b0-cd94-48ca-b74c-c83f62283d94/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36164/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:01:15,260] [INFO] Task succeeded: Blastn
[2023-03-18 21:01:15,261] [INFO] Selected 11 target genomes.
[2023-03-18 21:01:15,261] [INFO] Target genome list was writen to OceanDNA-b36164/target_genomes_gtdb.txt
[2023-03-18 21:01:15,297] [INFO] Task started: fastANI
[2023-03-18 21:01:15,297] [INFO] Running command: fastANI --query /var/lib/cwl/stg982bea73-ca27-4919-b851-dafe40f369f2/OceanDNA-b36164.fa --refList OceanDNA-b36164/target_genomes_gtdb.txt --output OceanDNA-b36164/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:01:23,700] [INFO] Task succeeded: fastANI
[2023-03-18 21:01:23,707] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 21:01:23,707] [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_002433465.1	s__Salinisphaera sp002433465	99.5878	859	1095	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002729955.1	s__Salinisphaera sp002729955	89.1478	944	1095	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000215955.2	s__Salinisphaera shabanensis	84.0009	807	1095	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017744135.1	s__Salinisphaera sp017744135	81.7997	688	1095	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003732545.1	s__Salinisphaera halophila	79.9936	570	1095	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	96.8739	N/A	N/A	N/A	N/A	1	-
GCF_003788635.1	s__Salinisphaera orenii	79.9875	585	1095	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	96.8739	N/A	N/A	N/A	N/A	1	-
GCF_000732535.1	s__Salinisphaera hydrothermalis	78.6588	351	1095	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003177035.1	s__Salinisphaera sp003177035	78.4708	357	1095	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003602005.1	s__Salinisphaera sp003602005	77.9571	325	1095	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013620825.1	s__Rhodanobacter sp001899565	75.5796	98	1095	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	98.48	98.45	0.90	0.89	4	-
GCF_003382365.1	s__Lysobacter silvisoli	75.5672	118	1095	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 21:01:23,710] [INFO] GTDB search result was written to OceanDNA-b36164/result_gtdb.tsv
[2023-03-18 21:01:23,713] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:01:23,719] [INFO] DFAST_QC result json was written to OceanDNA-b36164/dqc_result.json
[2023-03-18 21:01:23,719] [INFO] DFAST_QC completed!
[2023-03-18 21:01:23,719] [INFO] Total running time: 0h1m40s