[2023-07-01 07:29:15,349] [INFO] DFAST_QC pipeline started.
[2023-07-01 07:29:15,352] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 07:29:15,352] [INFO] DQC Reference Directory: /var/lib/cwl/stg80515316-e966-4b26-a0f7-f86f79412e14/dqc_reference
[2023-07-01 07:29:16,583] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 07:29:16,584] [INFO] Task started: Prodigal
[2023-07-01 07:29:16,584] [INFO] Running command: gunzip -c /var/lib/cwl/stg1a7c621e-4ccb-49b2-9db5-dc34efa91b1a/GCA_903893355.1_freshwater_MAG_---_MJ-2014-D2_bin-0309_genomic.fna.gz | prodigal -d GCA_903893355.1_freshwater_MAG_---_MJ-2014-D2_bin-0309_genomic.fna/cds.fna -a GCA_903893355.1_freshwater_MAG_---_MJ-2014-D2_bin-0309_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 07:29:20,875] [INFO] Task succeeded: Prodigal
[2023-07-01 07:29:20,875] [INFO] Task started: HMMsearch
[2023-07-01 07:29:20,875] [INFO] Running command: hmmsearch --tblout GCA_903893355.1_freshwater_MAG_---_MJ-2014-D2_bin-0309_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg80515316-e966-4b26-a0f7-f86f79412e14/dqc_reference/reference_markers.hmm GCA_903893355.1_freshwater_MAG_---_MJ-2014-D2_bin-0309_genomic.fna/protein.faa > /dev/null
[2023-07-01 07:29:21,232] [INFO] Task succeeded: HMMsearch
[2023-07-01 07:29:21,239] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1a7c621e-4ccb-49b2-9db5-dc34efa91b1a/GCA_903893355.1_freshwater_MAG_---_MJ-2014-D2_bin-0309_genomic.fna.gz]
[2023-07-01 07:29:21,262] [INFO] Query marker FASTA was written to GCA_903893355.1_freshwater_MAG_---_MJ-2014-D2_bin-0309_genomic.fna/markers.fasta
[2023-07-01 07:29:21,262] [INFO] Task started: Blastn
[2023-07-01 07:29:21,262] [INFO] Running command: blastn -query GCA_903893355.1_freshwater_MAG_---_MJ-2014-D2_bin-0309_genomic.fna/markers.fasta -db /var/lib/cwl/stg80515316-e966-4b26-a0f7-f86f79412e14/dqc_reference/reference_markers.fasta -out GCA_903893355.1_freshwater_MAG_---_MJ-2014-D2_bin-0309_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 07:29:22,058] [INFO] Task succeeded: Blastn
[2023-07-01 07:29:22,061] [INFO] Selected 22 target genomes.
[2023-07-01 07:29:22,061] [INFO] Target genome list was writen to GCA_903893355.1_freshwater_MAG_---_MJ-2014-D2_bin-0309_genomic.fna/target_genomes.txt
[2023-07-01 07:29:22,062] [INFO] Task started: fastANI
[2023-07-01 07:29:22,062] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a7c621e-4ccb-49b2-9db5-dc34efa91b1a/GCA_903893355.1_freshwater_MAG_---_MJ-2014-D2_bin-0309_genomic.fna.gz --refList GCA_903893355.1_freshwater_MAG_---_MJ-2014-D2_bin-0309_genomic.fna/target_genomes.txt --output GCA_903893355.1_freshwater_MAG_---_MJ-2014-D2_bin-0309_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 07:29:30,711] [INFO] Task succeeded: fastANI
[2023-07-01 07:29:30,711] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg80515316-e966-4b26-a0f7-f86f79412e14/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 07:29:30,712] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg80515316-e966-4b26-a0f7-f86f79412e14/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 07:29:30,727] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 07:29:30,727] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-07-01 07:29:30,727] [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
Polynucleobacter finlandensis	strain=MWH-Mekk-B1	GCA_018881755.1	1855894	1855894	type	True	82.7079	375	549	95	below_threshold
Polynucleobacter yangtzensis	strain=MWH-JaK3	GCA_001595965.1	1743159	1743159	type	True	79.5302	221	549	95	below_threshold
Polynucleobacter hirudinilacicola	strain=MWH-EgelM1-30-B4	GCA_002192535.1	1743166	1743166	type	True	79.338	242	549	95	below_threshold
Polynucleobacter sinensis	strain=MWH-HuW1	GCA_001595985.1	1743157	1743157	type	True	79.3284	219	549	95	below_threshold
Polynucleobacter ibericus	strain=es-MAR-2	GCA_018687955.1	1819725	1819725	type	True	79.3015	223	549	95	below_threshold
Polynucleobacter hallstattensis	strain=MWH-Hall10	GCA_018881835.1	1855586	1855586	type	True	79.274	223	549	95	below_threshold
Polynucleobacter wuianus	strain=QLW-P1FAT50C-4	GCA_001659725.1	1743168	1743168	type	True	79.204	222	549	95	below_threshold
Polynucleobacter arcticus	strain=UK-Long2-W17	GCA_013307205.1	1743165	1743165	type	True	79.1856	203	549	95	below_threshold
Polynucleobacter asymbioticus	strain=QLW-P1DMWA-1	GCA_000016345.1	576611	576611	type	True	79.1649	244	549	95	below_threshold
Polynucleobacter aenigmaticus	strain=MWH-K35W1	GCA_002206635.1	1743164	1743164	type	True	79.1268	237	549	95	below_threshold
Polynucleobacter alcilacus	strain=UK-Pondora-W15	GCA_018881545.1	1819739	1819739	type	True	79.0852	210	549	95	below_threshold
Polynucleobacter campilacus	strain=MWH-Feld-100	GCA_002206625.1	1743163	1743163	type	True	79.0242	231	549	95	below_threshold
Polynucleobacter duraquae	strain=MWH-MoK4	GCA_000973625.1	1835254	1835254	type	True	78.9999	227	549	95	below_threshold
Polynucleobacter bastaniensis	strain=AP-Basta-1000A-D1	GCA_018882205.1	2081039	2081039	type	True	78.9811	215	549	95	below_threshold
Polynucleobacter paludilacus	strain=MWH-Mekk-C3	GCA_018687595.1	1855895	1855895	type	True	78.9626	179	549	95	below_threshold
Polynucleobacter corsicus	strain=AP-Melu-1000-A1	GCA_018688255.1	2081042	2081042	type	True	78.9427	227	549	95	below_threshold
Polynucleobacter sphagniphilus	strain=MWH-Weng1-1	GCA_001953355.1	1743169	1743169	type	True	78.6845	196	549	95	below_threshold
Polynucleobacter tropicus	strain=MWH-UH21B	GCA_013307225.1	1743174	1743174	type	True	78.3594	209	549	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 07:29:30,729] [INFO] DFAST Taxonomy check result was written to GCA_903893355.1_freshwater_MAG_---_MJ-2014-D2_bin-0309_genomic.fna/tc_result.tsv
[2023-07-01 07:29:30,729] [INFO] ===== Taxonomy check completed =====
[2023-07-01 07:29:30,730] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 07:29:30,730] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg80515316-e966-4b26-a0f7-f86f79412e14/dqc_reference/checkm_data
[2023-07-01 07:29:30,731] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 07:29:30,753] [INFO] Task started: CheckM
[2023-07-01 07:29:30,753] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903893355.1_freshwater_MAG_---_MJ-2014-D2_bin-0309_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903893355.1_freshwater_MAG_---_MJ-2014-D2_bin-0309_genomic.fna/checkm_input GCA_903893355.1_freshwater_MAG_---_MJ-2014-D2_bin-0309_genomic.fna/checkm_result
[2023-07-01 07:29:50,478] [INFO] Task succeeded: CheckM
[2023-07-01 07:29:50,479] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.06%
Contamintation: 8.33%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-07-01 07:29:50,494] [INFO] ===== Completeness check finished =====
[2023-07-01 07:29:50,494] [INFO] ===== Start GTDB Search =====
[2023-07-01 07:29:50,495] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903893355.1_freshwater_MAG_---_MJ-2014-D2_bin-0309_genomic.fna/markers.fasta)
[2023-07-01 07:29:50,495] [INFO] Task started: Blastn
[2023-07-01 07:29:50,495] [INFO] Running command: blastn -query GCA_903893355.1_freshwater_MAG_---_MJ-2014-D2_bin-0309_genomic.fna/markers.fasta -db /var/lib/cwl/stg80515316-e966-4b26-a0f7-f86f79412e14/dqc_reference/reference_markers_gtdb.fasta -out GCA_903893355.1_freshwater_MAG_---_MJ-2014-D2_bin-0309_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 07:29:51,348] [INFO] Task succeeded: Blastn
[2023-07-01 07:29:51,352] [INFO] Selected 23 target genomes.
[2023-07-01 07:29:51,353] [INFO] Target genome list was writen to GCA_903893355.1_freshwater_MAG_---_MJ-2014-D2_bin-0309_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 07:29:51,353] [INFO] Task started: fastANI
[2023-07-01 07:29:51,354] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a7c621e-4ccb-49b2-9db5-dc34efa91b1a/GCA_903893355.1_freshwater_MAG_---_MJ-2014-D2_bin-0309_genomic.fna.gz --refList GCA_903893355.1_freshwater_MAG_---_MJ-2014-D2_bin-0309_genomic.fna/target_genomes_gtdb.txt --output GCA_903893355.1_freshwater_MAG_---_MJ-2014-D2_bin-0309_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 07:29:58,917] [INFO] Task succeeded: fastANI
[2023-07-01 07:29:58,931] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 07:29:58,932] [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_018881925.1	s__Polynucleobacter sp903880555	99.0973	496	549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	99.13	99.10	0.89	0.87	4	conclusive
GCF_018881755.1	s__Polynucleobacter sp903953215	82.7079	375	549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	98.19	97.38	0.93	0.86	15	-
GCA_903843235.1	s__Polynucleobacter sp903843235	81.7276	297	549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	99.64	99.31	0.88	0.84	5	-
GCA_903845455.1	s__Polynucleobacter sp903845455	81.0298	288	549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	98.50	98.25	0.75	0.69	7	-
GCA_903858445.1	s__Polynucleobacter sp903858445	80.1006	299	549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018882335.1	s__Polynucleobacter sp018882335	79.5878	245	549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018882365.1	s__Polynucleobacter sp018882365	79.5715	231	549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018882295.1	s__Polynucleobacter sp018882295	79.569	235	549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018882325.1	s__Polynucleobacter sp018882325	79.3687	233	549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018687815.1	s__Polynucleobacter sp018687815	79.3524	242	549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018687575.1	s__Polynucleobacter asymbioticus_C	79.3368	226	549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018688335.1	s__Polynucleobacter sp018688335	79.2989	225	549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	95.20	95.20	0.89	0.89	2	-
GCF_018881975.1	s__Polynucleobacter sp018881975	79.2175	228	549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018687975.1	s__Polynucleobacter sp018687975	79.1941	216	549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903827075.1	s__Polynucleobacter sp903827075	79.1689	194	549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	99.13	99.03	0.84	0.82	6	-
GCF_002206635.1	s__Polynucleobacter aenigmaticus	79.1268	237	549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903935355.1	s__Polynucleobacter sp903935355	78.991	211	549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	99.97	99.92	0.97	0.92	43	-
GCF_018882205.1	s__Polynucleobacter sp018882205	78.9811	215	549	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-07-01 07:29:58,933] [INFO] GTDB search result was written to GCA_903893355.1_freshwater_MAG_---_MJ-2014-D2_bin-0309_genomic.fna/result_gtdb.tsv
[2023-07-01 07:29:58,934] [INFO] ===== GTDB Search completed =====
[2023-07-01 07:29:58,938] [INFO] DFAST_QC result json was written to GCA_903893355.1_freshwater_MAG_---_MJ-2014-D2_bin-0309_genomic.fna/dqc_result.json
[2023-07-01 07:29:58,938] [INFO] DFAST_QC completed!
[2023-07-01 07:29:58,938] [INFO] Total running time: 0h0m44s