[2023-06-07 18:56:58,084] [INFO] DFAST_QC pipeline started.
[2023-06-07 18:56:58,088] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 18:56:58,088] [INFO] DQC Reference Directory: /var/lib/cwl/stg83122a49-c5b6-46ee-8e81-a7479494b00a/dqc_reference
[2023-06-07 18:56:59,418] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 18:56:59,419] [INFO] Task started: Prodigal
[2023-06-07 18:56:59,419] [INFO] Running command: gunzip -c /var/lib/cwl/stg1a995ebb-0274-4e6e-b7ea-b4eae5e41ca6/GCA_902752425.1_P2236_101_bin9_mag_fasta_genomic.fna.gz | prodigal -d GCA_902752425.1_P2236_101_bin9_mag_fasta_genomic.fna/cds.fna -a GCA_902752425.1_P2236_101_bin9_mag_fasta_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 18:57:03,470] [INFO] Task succeeded: Prodigal
[2023-06-07 18:57:03,470] [INFO] Task started: HMMsearch
[2023-06-07 18:57:03,471] [INFO] Running command: hmmsearch --tblout GCA_902752425.1_P2236_101_bin9_mag_fasta_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg83122a49-c5b6-46ee-8e81-a7479494b00a/dqc_reference/reference_markers.hmm GCA_902752425.1_P2236_101_bin9_mag_fasta_genomic.fna/protein.faa > /dev/null
[2023-06-07 18:57:03,718] [INFO] Task succeeded: HMMsearch
[2023-06-07 18:57:03,720] [INFO] Found 6/6 markers.
[2023-06-07 18:57:03,749] [INFO] Query marker FASTA was written to GCA_902752425.1_P2236_101_bin9_mag_fasta_genomic.fna/markers.fasta
[2023-06-07 18:57:03,750] [INFO] Task started: Blastn
[2023-06-07 18:57:03,750] [INFO] Running command: blastn -query GCA_902752425.1_P2236_101_bin9_mag_fasta_genomic.fna/markers.fasta -db /var/lib/cwl/stg83122a49-c5b6-46ee-8e81-a7479494b00a/dqc_reference/reference_markers.fasta -out GCA_902752425.1_P2236_101_bin9_mag_fasta_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 18:57:04,330] [INFO] Task succeeded: Blastn
[2023-06-07 18:57:04,334] [INFO] Selected 11 target genomes.
[2023-06-07 18:57:04,335] [INFO] Target genome list was writen to GCA_902752425.1_P2236_101_bin9_mag_fasta_genomic.fna/target_genomes.txt
[2023-06-07 18:57:04,337] [INFO] Task started: fastANI
[2023-06-07 18:57:04,337] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a995ebb-0274-4e6e-b7ea-b4eae5e41ca6/GCA_902752425.1_P2236_101_bin9_mag_fasta_genomic.fna.gz --refList GCA_902752425.1_P2236_101_bin9_mag_fasta_genomic.fna/target_genomes.txt --output GCA_902752425.1_P2236_101_bin9_mag_fasta_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 18:57:08,700] [INFO] Task succeeded: fastANI
[2023-06-07 18:57:08,700] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg83122a49-c5b6-46ee-8e81-a7479494b00a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 18:57:08,700] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg83122a49-c5b6-46ee-8e81-a7479494b00a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 18:57:08,710] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 18:57:08,711] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-07 18:57:08,711] [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	78.3469	180	591	95	below_threshold
Sulfurimonas gotlandica	strain=GD1	GCA_000242915.2	1176482	1176482	type	True	78.2211	218	591	95	below_threshold
Sulfurimonas gotlandica	strain=GD 1	GCA_000156095.1	1176482	1176482	type	True	78.1483	218	591	95	below_threshold
Candidatus Sulfurimonas marisnigri	strain=SoZ1	GCA_015265475.1	2740405	2740405	type	True	78.1304	204	591	95	below_threshold
Sulfurimonas hongkongensis	strain=AST-10	GCA_000445475.1	1172190	1172190	type	True	77.744	138	591	95	below_threshold
Sulfurimonas autotrophica	strain=DSM 16294	GCA_000147355.1	202747	202747	type	True	77.4014	144	591	95	below_threshold
Sulfurimonas xiamenensis	strain=1-1N	GCA_009258045.1	2590021	2590021	type	True	77.3444	138	591	95	below_threshold
Sulfurimonas denitrificans	strain=DSM 1251	GCA_000012965.1	39766	39766	type	True	77.3432	137	591	95	below_threshold
Sulfurimonas lithotrophica	strain=GYSZ_1	GCA_009258225.1	2590022	2590022	type	True	77.2795	109	591	95	below_threshold
Sulfurimonas crateris	strain=SN118	GCA_005217605.1	2574727	2574727	type	True	77.1678	114	591	95	below_threshold
Sulfurimonas hydrogeniphila	strain=NW10	GCA_009068765.1	2509341	2509341	type	True	77.1137	98	591	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-07 18:57:08,718] [INFO] DFAST Taxonomy check result was written to GCA_902752425.1_P2236_101_bin9_mag_fasta_genomic.fna/tc_result.tsv
[2023-06-07 18:57:08,719] [INFO] ===== Taxonomy check completed =====
[2023-06-07 18:57:08,719] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 18:57:08,719] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg83122a49-c5b6-46ee-8e81-a7479494b00a/dqc_reference/checkm_data
[2023-06-07 18:57:08,721] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 18:57:08,753] [INFO] Task started: CheckM
[2023-06-07 18:57:08,753] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902752425.1_P2236_101_bin9_mag_fasta_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902752425.1_P2236_101_bin9_mag_fasta_genomic.fna/checkm_input GCA_902752425.1_P2236_101_bin9_mag_fasta_genomic.fna/checkm_result
[2023-06-07 18:57:29,556] [INFO] Task succeeded: CheckM
[2023-06-07 18:57:29,557] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 12.50%
Strain heterogeneity: 42.86%
--------------------------------------------------------------------------------
[2023-06-07 18:57:29,579] [INFO] ===== Completeness check finished =====
[2023-06-07 18:57:29,580] [INFO] ===== Start GTDB Search =====
[2023-06-07 18:57:29,580] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902752425.1_P2236_101_bin9_mag_fasta_genomic.fna/markers.fasta)
[2023-06-07 18:57:29,580] [INFO] Task started: Blastn
[2023-06-07 18:57:29,581] [INFO] Running command: blastn -query GCA_902752425.1_P2236_101_bin9_mag_fasta_genomic.fna/markers.fasta -db /var/lib/cwl/stg83122a49-c5b6-46ee-8e81-a7479494b00a/dqc_reference/reference_markers_gtdb.fasta -out GCA_902752425.1_P2236_101_bin9_mag_fasta_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 18:57:30,367] [INFO] Task succeeded: Blastn
[2023-06-07 18:57:30,371] [INFO] Selected 15 target genomes.
[2023-06-07 18:57:30,371] [INFO] Target genome list was writen to GCA_902752425.1_P2236_101_bin9_mag_fasta_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 18:57:30,379] [INFO] Task started: fastANI
[2023-06-07 18:57:30,380] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a995ebb-0274-4e6e-b7ea-b4eae5e41ca6/GCA_902752425.1_P2236_101_bin9_mag_fasta_genomic.fna.gz --refList GCA_902752425.1_P2236_101_bin9_mag_fasta_genomic.fna/target_genomes_gtdb.txt --output GCA_902752425.1_P2236_101_bin9_mag_fasta_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 18:57:36,504] [INFO] Task succeeded: fastANI
[2023-06-07 18:57:36,524] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-07 18:57:36,524] [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_002781365.1	s__Sulfurimonas sp002781365	78.6819	184	591	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.99	99.89	0.98	0.96	19	-
GCA_002732645.1	s__Sulfurimonas sp002732645	78.5944	104	591	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	78.3537	179	591	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001873135.1	s__Sulfurimonas sp001873135	78.2623	191	591	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000242915.1	s__Sulfurimonas gotlandica	78.2211	218	591	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.99	99.99	1.00	1.00	2	-
GCA_018822665.1	s__Sulfurimonas sp018822665	78.1951	197	591	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.95	99.95	0.96	0.96	2	-
GCA_016744025.1	s__Sulfurimonas sp016744025	78.121	164	591	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	78.1132	205	591	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	78.0923	171	591	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018825665.1	s__Sulfurimonas sp018825665	77.6701	170	591	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	99.99	99.99	0.97	0.97	2	-
GCA_001829715.1	s__Sulfurimonas sp001829715	77.6698	133	591	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	98.65	98.65	0.90	0.90	2	-
GCF_009883775.1	s__Sulfurimonas sp002452895	77.4357	140	591	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	98.89	98.30	0.92	0.92	4	-
GCF_000147355.1	s__Sulfurimonas autotrophica	77.4014	144	591	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000012965.1	s__Sulfurimonas denitrificans	77.3432	137	591	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009068765.1	s__Sulfurimonas sp009068765	77.1165	97	591	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfurimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-07 18:57:36,526] [INFO] GTDB search result was written to GCA_902752425.1_P2236_101_bin9_mag_fasta_genomic.fna/result_gtdb.tsv
[2023-06-07 18:57:36,527] [INFO] ===== GTDB Search completed =====
[2023-06-07 18:57:36,530] [INFO] DFAST_QC result json was written to GCA_902752425.1_P2236_101_bin9_mag_fasta_genomic.fna/dqc_result.json
[2023-06-07 18:57:36,530] [INFO] DFAST_QC completed!
[2023-06-07 18:57:36,530] [INFO] Total running time: 0h0m38s