[2023-03-19 04:29:37,748] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:29:37,748] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:29:37,748] [INFO] DQC Reference Directory: /var/lib/cwl/stg533ef604-b6ea-4870-b03b-6e63e00d7c0f/dqc_reference
[2023-03-19 04:29:38,862] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:29:38,863] [INFO] Task started: Prodigal
[2023-03-19 04:29:38,864] [INFO] Running command: cat /var/lib/cwl/stg6e342dcd-6926-4a55-be9a-9fbcc470d391/OceanDNA-b13479.fa | prodigal -d OceanDNA-b13479/cds.fna -a OceanDNA-b13479/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:29:49,537] [INFO] Task succeeded: Prodigal
[2023-03-19 04:29:49,537] [INFO] Task started: HMMsearch
[2023-03-19 04:29:49,537] [INFO] Running command: hmmsearch --tblout OceanDNA-b13479/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg533ef604-b6ea-4870-b03b-6e63e00d7c0f/dqc_reference/reference_markers.hmm OceanDNA-b13479/protein.faa > /dev/null
[2023-03-19 04:29:49,700] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:29:49,701] [INFO] Found 6/6 markers.
[2023-03-19 04:29:49,715] [INFO] Query marker FASTA was written to OceanDNA-b13479/markers.fasta
[2023-03-19 04:29:49,715] [INFO] Task started: Blastn
[2023-03-19 04:29:49,715] [INFO] Running command: blastn -query OceanDNA-b13479/markers.fasta -db /var/lib/cwl/stg533ef604-b6ea-4870-b03b-6e63e00d7c0f/dqc_reference/reference_markers.fasta -out OceanDNA-b13479/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:29:50,228] [INFO] Task succeeded: Blastn
[2023-03-19 04:29:50,229] [INFO] Selected 15 target genomes.
[2023-03-19 04:29:50,229] [INFO] Target genome list was writen to OceanDNA-b13479/target_genomes.txt
[2023-03-19 04:29:50,238] [INFO] Task started: fastANI
[2023-03-19 04:29:50,238] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e342dcd-6926-4a55-be9a-9fbcc470d391/OceanDNA-b13479.fa --refList OceanDNA-b13479/target_genomes.txt --output OceanDNA-b13479/fastani_result.tsv --threads 1
[2023-03-19 04:29:55,062] [INFO] Task succeeded: fastANI
[2023-03-19 04:29:55,063] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg533ef604-b6ea-4870-b03b-6e63e00d7c0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:29:55,063] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg533ef604-b6ea-4870-b03b-6e63e00d7c0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:29:55,070] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:29:55,070] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 04:29:55,070] [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
Candidatus Sulfurimonas baltica	strain=GD2	GCA_015265455.1	2740404	2740404	type	True	77.355	94	654	95	below_threshold
Sulfurimonas xiamenensis	strain=1-1N	GCA_009258045.1	2590021	2590021	type	True	77.3048	64	654	95	below_threshold
Candidatus Sulfurimonas marisnigri	strain=SoZ1	GCA_015265475.1	2740405	2740405	type	True	77.1082	96	654	95	below_threshold
Sulfurimonas gotlandica	strain=GD 1	GCA_000156095.1	1176482	1176482	type	True	76.955	99	654	95	below_threshold
Sulfurimonas gotlandica	strain=GD1	GCA_000242915.2	1176482	1176482	type	True	76.9478	102	654	95	below_threshold
Sulfurimonas sediminis	strain=S2-6	GCA_014905115.1	2590020	2590020	type	True	76.7902	67	654	95	below_threshold
Sulfurimonas autotrophica	strain=DSM 16294	GCA_000147355.1	202747	202747	type	True	76.7271	96	654	95	below_threshold
Sulfurimonas denitrificans	strain=DSM 1251	GCA_000012965.1	39766	39766	type	True	76.7248	66	654	95	below_threshold
Sulfurimonas lithotrophica	strain=GYSZ_1	GCA_009258225.1	2590022	2590022	type	True	76.6339	60	654	95	below_threshold
Sulfurimonas hydrogeniphila	strain=NW10	GCA_009068765.1	2509341	2509341	type	True	76.605	72	654	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 04:29:55,070] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13479/tc_result.tsv
[2023-03-19 04:29:55,070] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:29:55,070] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:29:55,070] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg533ef604-b6ea-4870-b03b-6e63e00d7c0f/dqc_reference/checkm_data
[2023-03-19 04:29:55,071] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:29:55,074] [INFO] Task started: CheckM
[2023-03-19 04:29:55,074] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13479/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13479/checkm_input OceanDNA-b13479/checkm_result
[2023-03-19 04:30:25,914] [INFO] Task succeeded: CheckM
[2023-03-19 04:30:25,915] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.92%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:30:25,918] [INFO] ===== Completeness check finished =====
[2023-03-19 04:30:25,918] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:30:25,918] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13479/markers.fasta)
[2023-03-19 04:30:25,918] [INFO] Task started: Blastn
[2023-03-19 04:30:25,918] [INFO] Running command: blastn -query OceanDNA-b13479/markers.fasta -db /var/lib/cwl/stg533ef604-b6ea-4870-b03b-6e63e00d7c0f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13479/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:30:26,621] [INFO] Task succeeded: Blastn
[2023-03-19 04:30:26,622] [INFO] Selected 22 target genomes.
[2023-03-19 04:30:26,622] [INFO] Target genome list was writen to OceanDNA-b13479/target_genomes_gtdb.txt
[2023-03-19 04:30:26,664] [INFO] Task started: fastANI
[2023-03-19 04:30:26,664] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e342dcd-6926-4a55-be9a-9fbcc470d391/OceanDNA-b13479.fa --refList OceanDNA-b13479/target_genomes_gtdb.txt --output OceanDNA-b13479/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:30:34,335] [INFO] Task succeeded: fastANI
[2023-03-19 04:30:34,345] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 04:30:34,345] [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_001873135.1	s__Sulfurimonas sp001873135	77.6156	90	654	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011391635.1	s__Sulfurimonas sp011391635	77.4455	76	654	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015265455.1	s__Sulfurimonas baltica	77.3381	93	654	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015487265.1	s__Sulfurimonas sp015487265	77.3067	87	654	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017357825.1	s__Sulfurimonas sp017357825	77.2032	113	654	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001829625.1	s__Sulfurimonas sp001829625	77.1827	82	654	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.76	99.76	0.87	0.87	2	-
GCA_016744025.1	s__Sulfurimonas sp016744025	77.1691	83	654	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018698455.1	s__Sulfurimonas sp018698455	77.0991	95	654	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002781365.1	s__Sulfurimonas sp002781365	77.0174	90	654	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.99	99.89	0.98	0.96	19	-
GCF_000242915.1	s__Sulfurimonas gotlandica	76.9478	102	654	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.99	99.99	1.00	1.00	2	-
GCA_018825665.1	s__Sulfurimonas sp018825665	76.823	63	654	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.99	99.99	0.97	0.97	2	-
GCA_018822665.1	s__Sulfurimonas sp018822665	76.7274	92	654	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.95	99.95	0.96	0.96	2	-
GCF_000147355.1	s__Sulfurimonas autotrophica	76.7271	96	654	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001829715.1	s__Sulfurimonas sp001829715	76.6827	68	654	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	98.65	98.65	0.90	0.90	2	-
GCA_001829675.1	s__Sulfurimonas sp001829675	76.6391	71	654	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.77	99.75	0.96	0.96	4	-
GCF_009258225.1	s__Sulfurimonas sp009258225	76.6339	60	654	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903892995.1	s__CAITKP01 sp903892995	76.3455	52	654	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__CAITKP01	95.0	99.47	98.97	0.95	0.95	3	-
--------------------------------------------------------------------------------
[2023-03-19 04:30:34,345] [INFO] GTDB search result was written to OceanDNA-b13479/result_gtdb.tsv
[2023-03-19 04:30:34,346] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:30:34,347] [INFO] DFAST_QC result json was written to OceanDNA-b13479/dqc_result.json
[2023-03-19 04:30:34,347] [INFO] DFAST_QC completed!
[2023-03-19 04:30:34,347] [INFO] Total running time: 0h0m57s