[2024-01-24 13:09:29,217] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:29,219] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:29,219] [INFO] DQC Reference Directory: /var/lib/cwl/stgfe215419-6105-4309-af78-3a56e7427674/dqc_reference
[2024-01-24 13:09:30,492] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:30,493] [INFO] Task started: Prodigal
[2024-01-24 13:09:30,493] [INFO] Running command: gunzip -c /var/lib/cwl/stgb4d31c1d-b903-4033-bd01-cc0bb3f9b0c9/GCF_000338295.1_First_genomic.fna.gz | prodigal -d GCF_000338295.1_First_genomic.fna/cds.fna -a GCF_000338295.1_First_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:05,413] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:05,414] [INFO] Task started: HMMsearch
[2024-01-24 13:10:05,414] [INFO] Running command: hmmsearch --tblout GCF_000338295.1_First_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfe215419-6105-4309-af78-3a56e7427674/dqc_reference/reference_markers.hmm GCF_000338295.1_First_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:05,853] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:05,855] [INFO] Found 6/6 markers.
[2024-01-24 13:10:05,915] [INFO] Query marker FASTA was written to GCF_000338295.1_First_genomic.fna/markers.fasta
[2024-01-24 13:10:05,915] [INFO] Task started: Blastn
[2024-01-24 13:10:05,915] [INFO] Running command: blastn -query GCF_000338295.1_First_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe215419-6105-4309-af78-3a56e7427674/dqc_reference/reference_markers.fasta -out GCF_000338295.1_First_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:06,536] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:06,543] [INFO] Selected 13 target genomes.
[2024-01-24 13:10:06,544] [INFO] Target genome list was writen to GCF_000338295.1_First_genomic.fna/target_genomes.txt
[2024-01-24 13:10:06,553] [INFO] Task started: fastANI
[2024-01-24 13:10:06,554] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4d31c1d-b903-4033-bd01-cc0bb3f9b0c9/GCF_000338295.1_First_genomic.fna.gz --refList GCF_000338295.1_First_genomic.fna/target_genomes.txt --output GCF_000338295.1_First_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:25,481] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:25,482] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfe215419-6105-4309-af78-3a56e7427674/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:25,482] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfe215419-6105-4309-af78-3a56e7427674/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:25,495] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:10:25,495] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:25,496] [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
Rhodopirellula europaea	strain=6C	GCA_000338295.1	1263866	1263866	type	True	100.0	2253	2265	95	conclusive
Rhodopirellula baltica	strain=1	GCA_000196115.1	265606	265606	type	True	88.8556	1873	2265	95	below_threshold
Rhodopirellula bahusiensis	strain=SWK21	GCA_002727185.1	2014065	2014065	type	True	87.2188	1746	2265	95	below_threshold
Rhodopirellula islandica	strain=K833	GCA_001027925.1	595434	595434	type	True	83.5867	1554	2265	95	below_threshold
Rhodopirellula sallentina	strain=SM41	GCA_000346505.1	1263869	1263869	type	True	77.7609	283	2265	95	below_threshold
Rhodopirellula aestuarii	strain=ICT_H3.1	GCA_023701485.1	2950107	2950107	type	True	77.5731	261	2265	95	below_threshold
Crateriforma conspicua	strain=Mal65	GCA_007752935.1	2527996	2527996	type	True	77.5461	217	2265	95	below_threshold
Rubripirellula obstinata	strain=CECT 8602	GCA_001642955.1	406547	406547	type	True	77.3094	160	2265	95	below_threshold
Rhodopirellula rubra	strain=CECT 8075	GCA_014192335.1	980271	980271	type	True	77.2501	286	2265	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:25,497] [INFO] DFAST Taxonomy check result was written to GCF_000338295.1_First_genomic.fna/tc_result.tsv
[2024-01-24 13:10:25,498] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:25,498] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:25,498] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfe215419-6105-4309-af78-3a56e7427674/dqc_reference/checkm_data
[2024-01-24 13:10:25,499] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:25,567] [INFO] Task started: CheckM
[2024-01-24 13:10:25,567] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000338295.1_First_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000338295.1_First_genomic.fna/checkm_input GCF_000338295.1_First_genomic.fna/checkm_result
[2024-01-24 13:12:14,987] [INFO] Task succeeded: CheckM
[2024-01-24 13:12:14,988] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:12:15,013] [INFO] ===== Completeness check finished =====
[2024-01-24 13:12:15,014] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:12:15,014] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000338295.1_First_genomic.fna/markers.fasta)
[2024-01-24 13:12:15,015] [INFO] Task started: Blastn
[2024-01-24 13:12:15,015] [INFO] Running command: blastn -query GCF_000338295.1_First_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe215419-6105-4309-af78-3a56e7427674/dqc_reference/reference_markers_gtdb.fasta -out GCF_000338295.1_First_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:12:15,839] [INFO] Task succeeded: Blastn
[2024-01-24 13:12:15,843] [INFO] Selected 10 target genomes.
[2024-01-24 13:12:15,843] [INFO] Target genome list was writen to GCF_000338295.1_First_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:12:15,899] [INFO] Task started: fastANI
[2024-01-24 13:12:15,899] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4d31c1d-b903-4033-bd01-cc0bb3f9b0c9/GCF_000338295.1_First_genomic.fna.gz --refList GCF_000338295.1_First_genomic.fna/target_genomes_gtdb.txt --output GCF_000338295.1_First_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:12:31,312] [INFO] Task succeeded: fastANI
[2024-01-24 13:12:31,331] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:12:31,331] [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_000338295.1	s__Rhodopirellula europaea	100.0	2253	2265	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	96.18	96.16	0.87	0.86	3	conclusive
GCF_000196115.1	s__Rhodopirellula baltica	88.8657	1871	2265	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	97.96	97.13	0.94	0.89	5	-
GCF_002727185.1	s__Rhodopirellula bahusiensis	87.2184	1747	2265	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001027925.1	s__Rhodopirellula islandica	83.5813	1555	2265	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000346505.1	s__Rhodopirellula sallentina	77.75	284	2265	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859915.1	s__Rhodopirellula pilleata	77.6454	292	2265	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007752935.1	s__Crateriforma conspicua	77.5461	217	2265	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Crateriforma	95.0	98.96	98.96	0.93	0.93	2	-
GCF_014192335.1	s__Rhodopirellula rubra	77.2292	285	2265	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	95.37	95.37	0.86	0.86	2	-
GCF_012290005.1	s__Crateriforma spongiae	76.7841	223	2265	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Crateriforma	95.0	98.43	98.43	0.93	0.93	2	-
GCF_002289565.1	s__Stieleria sp002289565	76.3434	211	2265	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:12:31,333] [INFO] GTDB search result was written to GCF_000338295.1_First_genomic.fna/result_gtdb.tsv
[2024-01-24 13:12:31,334] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:12:31,338] [INFO] DFAST_QC result json was written to GCF_000338295.1_First_genomic.fna/dqc_result.json
[2024-01-24 13:12:31,339] [INFO] DFAST_QC completed!
[2024-01-24 13:12:31,339] [INFO] Total running time: 0h3m2s