[2024-01-24 11:51:50,525] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:50,527] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:50,527] [INFO] DQC Reference Directory: /var/lib/cwl/stg37ae0fd9-1394-41c8-b813-0e48a62ca22e/dqc_reference
[2024-01-24 11:51:51,730] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:51,731] [INFO] Task started: Prodigal
[2024-01-24 11:51:51,731] [INFO] Running command: gunzip -c /var/lib/cwl/stg1d929ef4-5e43-41f5-9f6c-e09345055bb7/GCF_019457985.1_ASM1945798v1_genomic.fna.gz | prodigal -d GCF_019457985.1_ASM1945798v1_genomic.fna/cds.fna -a GCF_019457985.1_ASM1945798v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:52:18,025] [INFO] Task succeeded: Prodigal
[2024-01-24 11:52:18,026] [INFO] Task started: HMMsearch
[2024-01-24 11:52:18,026] [INFO] Running command: hmmsearch --tblout GCF_019457985.1_ASM1945798v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg37ae0fd9-1394-41c8-b813-0e48a62ca22e/dqc_reference/reference_markers.hmm GCF_019457985.1_ASM1945798v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:52:18,337] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:52:18,340] [INFO] Found 6/6 markers.
[2024-01-24 11:52:18,384] [INFO] Query marker FASTA was written to GCF_019457985.1_ASM1945798v1_genomic.fna/markers.fasta
[2024-01-24 11:52:18,384] [INFO] Task started: Blastn
[2024-01-24 11:52:18,384] [INFO] Running command: blastn -query GCF_019457985.1_ASM1945798v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg37ae0fd9-1394-41c8-b813-0e48a62ca22e/dqc_reference/reference_markers.fasta -out GCF_019457985.1_ASM1945798v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:19,044] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:19,048] [INFO] Selected 10 target genomes.
[2024-01-24 11:52:19,049] [INFO] Target genome list was writen to GCF_019457985.1_ASM1945798v1_genomic.fna/target_genomes.txt
[2024-01-24 11:52:19,058] [INFO] Task started: fastANI
[2024-01-24 11:52:19,059] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d929ef4-5e43-41f5-9f6c-e09345055bb7/GCF_019457985.1_ASM1945798v1_genomic.fna.gz --refList GCF_019457985.1_ASM1945798v1_genomic.fna/target_genomes.txt --output GCF_019457985.1_ASM1945798v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:28,190] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:28,191] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg37ae0fd9-1394-41c8-b813-0e48a62ca22e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:28,191] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg37ae0fd9-1394-41c8-b813-0e48a62ca22e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:28,204] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:52:28,205] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:52:28,205] [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
Muricauda oceani	strain=501str8	GCA_019457985.1	2698672	2698672	type	True	100.0	1484	1488	95	conclusive
Muricauda oceani	strain=501str8	GCA_011068285.1	2698672	2698672	type	True	99.9945	1487	1488	95	conclusive
Muricauda aurea	strain=BC31-1-A7	GCA_017313785.1	2915619	2915619	type	True	85.1916	977	1488	95	below_threshold
Muricauda brasiliensis	strain=K001	GCA_003057865.1	2162892	2162892	type	True	85.1855	918	1488	95	below_threshold
Muricauda chongwuensis	strain=HICW	GCA_013376415.1	2697365	2697365	type	True	84.9462	893	1488	95	below_threshold
Muricauda profundi	strain=BC31-3-A3	GCA_017313275.1	2915620	2915620	type	True	82.9182	783	1488	95	below_threshold
Muricauda oceanensis	strain=40DY170	GCA_003992595.1	2499163	2499163	type	True	82.9062	815	1488	95	below_threshold
Muricauda hadalis	strain=MT-229	GCA_007785775.2	2597517	2597517	type	True	79.8286	552	1488	95	below_threshold
Muricauda amoyensis	strain=GCL-11	GCA_003058265.1	2169401	2169401	type	True	79.1625	533	1488	95	below_threshold
Muricauda hymeniacidonis	strain=176CP4-71	GCA_004296335.1	2517819	2517819	type	True	77.0656	202	1488	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:28,206] [INFO] DFAST Taxonomy check result was written to GCF_019457985.1_ASM1945798v1_genomic.fna/tc_result.tsv
[2024-01-24 11:52:28,207] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:28,207] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:28,207] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg37ae0fd9-1394-41c8-b813-0e48a62ca22e/dqc_reference/checkm_data
[2024-01-24 11:52:28,208] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:28,447] [INFO] Task started: CheckM
[2024-01-24 11:52:28,447] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019457985.1_ASM1945798v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019457985.1_ASM1945798v1_genomic.fna/checkm_input GCF_019457985.1_ASM1945798v1_genomic.fna/checkm_result
[2024-01-24 11:53:39,975] [INFO] Task succeeded: CheckM
[2024-01-24 11:53:39,977] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:53:39,999] [INFO] ===== Completeness check finished =====
[2024-01-24 11:53:39,999] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:53:39,999] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019457985.1_ASM1945798v1_genomic.fna/markers.fasta)
[2024-01-24 11:53:40,000] [INFO] Task started: Blastn
[2024-01-24 11:53:40,000] [INFO] Running command: blastn -query GCF_019457985.1_ASM1945798v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg37ae0fd9-1394-41c8-b813-0e48a62ca22e/dqc_reference/reference_markers_gtdb.fasta -out GCF_019457985.1_ASM1945798v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:53:40,832] [INFO] Task succeeded: Blastn
[2024-01-24 11:53:40,838] [INFO] Selected 9 target genomes.
[2024-01-24 11:53:40,838] [INFO] Target genome list was writen to GCF_019457985.1_ASM1945798v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:53:40,846] [INFO] Task started: fastANI
[2024-01-24 11:53:40,846] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d929ef4-5e43-41f5-9f6c-e09345055bb7/GCF_019457985.1_ASM1945798v1_genomic.fna.gz --refList GCF_019457985.1_ASM1945798v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019457985.1_ASM1945798v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:53:49,417] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:49,432] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:53:49,432] [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_011068285.1	s__Muricauda sp011068285	99.9945	1487	1488	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017313785.1	s__Muricauda sp002711825	85.194	977	1488	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	98.76	98.31	0.81	0.77	4	-
GCF_003057865.1	s__Muricauda brasiliensis	85.1925	918	1488	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	96.90	96.90	0.89	0.89	2	-
GCF_017313275.1	s__Muricauda lutimaris_A	82.9182	783	1488	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003992595.1	s__Muricauda sp002452975	82.888	816	1488	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	99.01	99.01	0.89	0.89	2	-
GCF_010468565.1	s__Muricauda sp010468565	82.7433	805	1488	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911645.1	s__Muricauda sp013911645	82.3541	803	1488	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000224085.1	s__Muricauda ruestringensis	82.2518	778	1488	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017313105.1	s__Muricauda sp017313105	82.0188	712	1488	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:53:49,433] [INFO] GTDB search result was written to GCF_019457985.1_ASM1945798v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:53:49,434] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:53:49,437] [INFO] DFAST_QC result json was written to GCF_019457985.1_ASM1945798v1_genomic.fna/dqc_result.json
[2024-01-24 11:53:49,437] [INFO] DFAST_QC completed!
[2024-01-24 11:53:49,437] [INFO] Total running time: 0h1m59s