[2023-03-17 04:15:15,095] [INFO] DFAST_QC pipeline started.
[2023-03-17 04:15:15,095] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 04:15:15,095] [INFO] DQC Reference Directory: /var/lib/cwl/stg2dbd5a36-7e02-463d-b963-d02506715f42/dqc_reference
[2023-03-17 04:15:16,760] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 04:15:16,760] [INFO] Task started: Prodigal
[2023-03-17 04:15:16,760] [INFO] Running command: cat /var/lib/cwl/stg5d252ab5-72fd-4aa2-ae12-cf58007a9552/OceanDNA-b13464.fa | prodigal -d OceanDNA-b13464/cds.fna -a OceanDNA-b13464/protein.faa -g 11 -q > /dev/null
[2023-03-17 04:15:27,078] [INFO] Task succeeded: Prodigal
[2023-03-17 04:15:27,079] [INFO] Task started: HMMsearch
[2023-03-17 04:15:27,079] [INFO] Running command: hmmsearch --tblout OceanDNA-b13464/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2dbd5a36-7e02-463d-b963-d02506715f42/dqc_reference/reference_markers.hmm OceanDNA-b13464/protein.faa > /dev/null
[2023-03-17 04:15:27,247] [INFO] Task succeeded: HMMsearch
[2023-03-17 04:15:27,248] [INFO] Found 6/6 markers.
[2023-03-17 04:15:27,262] [INFO] Query marker FASTA was written to OceanDNA-b13464/markers.fasta
[2023-03-17 04:15:27,262] [INFO] Task started: Blastn
[2023-03-17 04:15:27,262] [INFO] Running command: blastn -query OceanDNA-b13464/markers.fasta -db /var/lib/cwl/stg2dbd5a36-7e02-463d-b963-d02506715f42/dqc_reference/reference_markers.fasta -out OceanDNA-b13464/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:15:27,781] [INFO] Task succeeded: Blastn
[2023-03-17 04:15:27,782] [INFO] Selected 15 target genomes.
[2023-03-17 04:15:27,782] [INFO] Target genome list was writen to OceanDNA-b13464/target_genomes.txt
[2023-03-17 04:15:27,790] [INFO] Task started: fastANI
[2023-03-17 04:15:27,791] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d252ab5-72fd-4aa2-ae12-cf58007a9552/OceanDNA-b13464.fa --refList OceanDNA-b13464/target_genomes.txt --output OceanDNA-b13464/fastani_result.tsv --threads 1
[2023-03-17 04:15:34,190] [INFO] Task succeeded: fastANI
[2023-03-17 04:15:34,191] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2dbd5a36-7e02-463d-b963-d02506715f42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 04:15:34,191] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2dbd5a36-7e02-463d-b963-d02506715f42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 04:15:34,199] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 04:15:34,199] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 04:15:34,199] [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
Sulfurimonas indica	strain=NW8N	GCA_009192995.1	2508707	2508707	type	True	78.2321	176	667	95	below_threshold
Sulfurimonas autotrophica	strain=DSM 16294	GCA_000147355.1	202747	202747	type	True	78.1133	189	667	95	below_threshold
Sulfurimonas gotlandica	strain=GD1	GCA_000242915.2	1176482	1176482	type	True	78.0179	222	667	95	below_threshold
Sulfurimonas gotlandica	strain=GD 1	GCA_000156095.1	1176482	1176482	type	True	77.9811	220	667	95	below_threshold
Candidatus Sulfurimonas baltica	strain=GD2	GCA_015265455.1	2740404	2740404	type	True	77.694	172	667	95	below_threshold
Candidatus Sulfurimonas marisnigri	strain=SoZ1	GCA_015265475.1	2740405	2740405	type	True	77.6041	182	667	95	below_threshold
Sulfurimonas paralvinellae	strain=GO25	GCA_014905135.1	317658	317658	type	True	77.5292	149	667	95	below_threshold
Sulfurimonas hydrogeniphila	strain=NW10	GCA_009068765.1	2509341	2509341	type	True	77.4114	119	667	95	below_threshold
Sulfurimonas sediminis	strain=S2-6	GCA_014905115.1	2590020	2590020	type	True	77.4069	135	667	95	below_threshold
Sulfurimonas crateris	strain=SN118	GCA_005217605.1	2574727	2574727	type	True	77.2874	76	667	95	below_threshold
Sulfurimonas hongkongensis	strain=AST-10	GCA_000445475.1	1172190	1172190	type	True	77.2567	155	667	95	below_threshold
Sulfurimonas lithotrophica	strain=GYSZ_1	GCA_009258225.1	2590022	2590022	type	True	76.9435	129	667	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 04:15:34,200] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13464/tc_result.tsv
[2023-03-17 04:15:34,200] [INFO] ===== Taxonomy check completed =====
[2023-03-17 04:15:34,200] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 04:15:34,200] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2dbd5a36-7e02-463d-b963-d02506715f42/dqc_reference/checkm_data
[2023-03-17 04:15:34,201] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 04:15:34,204] [INFO] Task started: CheckM
[2023-03-17 04:15:34,204] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13464/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13464/checkm_input OceanDNA-b13464/checkm_result
[2023-03-17 04:16:04,102] [INFO] Task succeeded: CheckM
[2023-03-17 04:16:04,102] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.14%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 04:16:04,104] [INFO] ===== Completeness check finished =====
[2023-03-17 04:16:04,104] [INFO] ===== Start GTDB Search =====
[2023-03-17 04:16:04,104] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13464/markers.fasta)
[2023-03-17 04:16:04,105] [INFO] Task started: Blastn
[2023-03-17 04:16:04,105] [INFO] Running command: blastn -query OceanDNA-b13464/markers.fasta -db /var/lib/cwl/stg2dbd5a36-7e02-463d-b963-d02506715f42/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13464/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:16:04,841] [INFO] Task succeeded: Blastn
[2023-03-17 04:16:04,842] [INFO] Selected 20 target genomes.
[2023-03-17 04:16:04,842] [INFO] Target genome list was writen to OceanDNA-b13464/target_genomes_gtdb.txt
[2023-03-17 04:16:05,160] [INFO] Task started: fastANI
[2023-03-17 04:16:05,160] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d252ab5-72fd-4aa2-ae12-cf58007a9552/OceanDNA-b13464.fa --refList OceanDNA-b13464/target_genomes_gtdb.txt --output OceanDNA-b13464/fastani_result_gtdb.tsv --threads 1
[2023-03-17 04:16:12,618] [INFO] Task succeeded: fastANI
[2023-03-17 04:16:12,629] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 04:16:12,630] [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_015487265.1	s__Sulfurimonas sp015487265	79.9462	304	667	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002335055.1	s__Sulfurimonas sp002335055	78.9385	219	667	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.96	99.95	0.96	0.95	3	-
GCA_002733945.2	s__Sulfurimonas sp002733945	78.8601	221	667	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015488615.1	s__Sulfurimonas sp015488615	78.5644	196	667	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.68	99.68	0.82	0.82	2	-
GCA_018698455.1	s__Sulfurimonas sp018698455	78.533	228	667	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	78.5224	237	667	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009192995.1	s__Sulfurimonas indica	78.1903	178	667	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000147355.1	s__Sulfurimonas autotrophica	78.1203	188	667	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014381585.1	s__Sulfurimonas ponti	77.9593	154	667	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.38	99.38	0.90	0.90	2	-
GCA_016744025.1	s__Sulfurimonas sp016744025	77.9116	211	667	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013153755.1	s__Sulfurimonas sp013153755	77.9087	176	667	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015487435.1	s__Sulfurimonas sp015487435	77.8245	173	667	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	77.7175	140	667	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.76	99.76	0.87	0.87	2	-
GCA_002732645.1	s__Sulfurimonas sp002732645	77.7042	124	667	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013607665.1	s__Sulfurimonas sp013607665	77.6599	128	667	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015265475.1	s__Sulfurimonas marisnigri	77.6041	182	667	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014905135.1	s__Sulfurimonas paralvinellae	77.5292	149	667	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015662405.1	s__Sulfurimonas autotrophica_A	77.3626	129	667	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733155.1	s__Sulfurimonas sp002733155	77.2544	156	667	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009258225.1	s__Sulfurimonas sp009258225	76.9435	129	667	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 04:16:12,630] [INFO] GTDB search result was written to OceanDNA-b13464/result_gtdb.tsv
[2023-03-17 04:16:12,630] [INFO] ===== GTDB Search completed =====
[2023-03-17 04:16:12,632] [INFO] DFAST_QC result json was written to OceanDNA-b13464/dqc_result.json
[2023-03-17 04:16:12,632] [INFO] DFAST_QC completed!
[2023-03-17 04:16:12,632] [INFO] Total running time: 0h0m58s