[2023-06-29 18:14:47,747] [INFO] DFAST_QC pipeline started.
[2023-06-29 18:14:47,755] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 18:14:47,755] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc4679c7-7306-4524-bbac-e9a6e7cc21f2/dqc_reference
[2023-06-29 18:14:49,049] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 18:14:49,050] [INFO] Task started: Prodigal
[2023-06-29 18:14:49,051] [INFO] Running command: gunzip -c /var/lib/cwl/stgc4984690-14e2-45fe-bd83-160ae9a54f20/GCA_937873685.1_SRR2107183_bin.57_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937873685.1_SRR2107183_bin.57_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937873685.1_SRR2107183_bin.57_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 18:15:01,025] [INFO] Task succeeded: Prodigal
[2023-06-29 18:15:01,026] [INFO] Task started: HMMsearch
[2023-06-29 18:15:01,026] [INFO] Running command: hmmsearch --tblout GCA_937873685.1_SRR2107183_bin.57_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc4679c7-7306-4524-bbac-e9a6e7cc21f2/dqc_reference/reference_markers.hmm GCA_937873685.1_SRR2107183_bin.57_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 18:15:01,296] [INFO] Task succeeded: HMMsearch
[2023-06-29 18:15:01,298] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc4984690-14e2-45fe-bd83-160ae9a54f20/GCA_937873685.1_SRR2107183_bin.57_CONCOCT_v1.1_MAG_genomic.fna.gz]
[2023-06-29 18:15:01,344] [INFO] Query marker FASTA was written to GCA_937873685.1_SRR2107183_bin.57_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-29 18:15:01,345] [INFO] Task started: Blastn
[2023-06-29 18:15:01,345] [INFO] Running command: blastn -query GCA_937873685.1_SRR2107183_bin.57_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc4679c7-7306-4524-bbac-e9a6e7cc21f2/dqc_reference/reference_markers.fasta -out GCA_937873685.1_SRR2107183_bin.57_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 18:15:02,347] [INFO] Task succeeded: Blastn
[2023-06-29 18:15:02,352] [INFO] Selected 23 target genomes.
[2023-06-29 18:15:02,353] [INFO] Target genome list was writen to GCA_937873685.1_SRR2107183_bin.57_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-29 18:15:02,355] [INFO] Task started: fastANI
[2023-06-29 18:15:02,356] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4984690-14e2-45fe-bd83-160ae9a54f20/GCA_937873685.1_SRR2107183_bin.57_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937873685.1_SRR2107183_bin.57_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937873685.1_SRR2107183_bin.57_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 18:15:24,984] [INFO] Task succeeded: fastANI
[2023-06-29 18:15:24,984] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc4679c7-7306-4524-bbac-e9a6e7cc21f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 18:15:24,985] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc4679c7-7306-4524-bbac-e9a6e7cc21f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 18:15:25,010] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 18:15:25,010] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 18:15:25,010] [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
Mesorhizobium composti	strain=CC-YTH430	GCA_004801285.1	2675109	2675109	type	True	78.6169	419	1227	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	78.2937	495	1227	95	below_threshold
Aquibium carbonis	strain=B2.3	GCA_003970795.1	2495581	2495581	type	True	78.2704	419	1227	95	below_threshold
Nitratireductor soli	strain=ZZ-1	GCA_001050155.1	1670619	1670619	type	True	78.2237	387	1227	95	below_threshold
Nitratireductor pacificus	strain=pht-3B	GCA_000300335.1	1231180	1231180	type	True	78.1428	378	1227	95	below_threshold
Mesorhizobium silamurunense	strain=CCBAU 01550	GCA_014843825.1	499528	499528	type	True	78.1132	421	1227	95	below_threshold
Mesorhizobium atlanticum	strain=CNPSo 3140	GCA_003289965.1	2233532	2233532	type	True	78.0983	440	1227	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	77.9947	423	1227	95	below_threshold
Mesorhizobium camelthorni	strain=CCNWXJ 40-4	GCA_011045125.1	475069	475069	type	True	77.9047	403	1227	95	below_threshold
Nitratireductor arenosus	strain=CAU 1489	GCA_009742725.1	2682096	2682096	type	True	77.9026	383	1227	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	77.8998	401	1227	95	below_threshold
Mesorhizobium helmanticense	strain=CSLC115N	GCA_003034915.1	1776423	1776423	type	True	77.868	400	1227	95	below_threshold
Mesorhizobium tamadayense	strain=DSM 28320	GCA_003863365.1	425306	425306	type	True	77.8548	434	1227	95	below_threshold
Mesorhizobium wenxiniae	strain=WYCCWR 10195	GCA_002284535.1	2014805	2014805	type	True	77.8371	402	1227	95	below_threshold
Oricola thermophila	strain=MEBiC13590	GCA_013358405.1	2742145	2742145	type	True	77.8142	334	1227	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	77.7989	344	1227	95	below_threshold
Mesorhizobium caraganae	strain=LMG 24397	GCA_016836705.1	483206	483206	type	True	77.7862	439	1227	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	77.7469	348	1227	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	77.7377	349	1227	95	below_threshold
Mesorhizobium muleiense	strain=CGMCC 1.11022	GCA_900099905.1	1004279	1004279	type	True	77.7304	399	1227	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	77.7211	445	1227	95	below_threshold
Oricola indica	strain=JL-62	GCA_019966595.1	2872591	2872591	type	True	77.7201	378	1227	95	below_threshold
Aminobacter niigataensis	strain=DSM 7050	GCA_014200015.1	83265	83265	type	True	77.705	404	1227	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 18:15:25,013] [INFO] DFAST Taxonomy check result was written to GCA_937873685.1_SRR2107183_bin.57_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-29 18:15:25,013] [INFO] ===== Taxonomy check completed =====
[2023-06-29 18:15:25,014] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 18:15:25,014] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc4679c7-7306-4524-bbac-e9a6e7cc21f2/dqc_reference/checkm_data
[2023-06-29 18:15:25,016] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 18:15:25,057] [INFO] Task started: CheckM
[2023-06-29 18:15:25,057] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937873685.1_SRR2107183_bin.57_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937873685.1_SRR2107183_bin.57_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937873685.1_SRR2107183_bin.57_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-29 18:16:03,020] [INFO] Task succeeded: CheckM
[2023-06-29 18:16:03,022] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.74%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 18:16:03,048] [INFO] ===== Completeness check finished =====
[2023-06-29 18:16:03,048] [INFO] ===== Start GTDB Search =====
[2023-06-29 18:16:03,049] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937873685.1_SRR2107183_bin.57_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-29 18:16:03,049] [INFO] Task started: Blastn
[2023-06-29 18:16:03,049] [INFO] Running command: blastn -query GCA_937873685.1_SRR2107183_bin.57_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc4679c7-7306-4524-bbac-e9a6e7cc21f2/dqc_reference/reference_markers_gtdb.fasta -out GCA_937873685.1_SRR2107183_bin.57_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 18:16:05,018] [INFO] Task succeeded: Blastn
[2023-06-29 18:16:05,023] [INFO] Selected 24 target genomes.
[2023-06-29 18:16:05,024] [INFO] Target genome list was writen to GCA_937873685.1_SRR2107183_bin.57_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 18:16:05,041] [INFO] Task started: fastANI
[2023-06-29 18:16:05,041] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4984690-14e2-45fe-bd83-160ae9a54f20/GCA_937873685.1_SRR2107183_bin.57_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937873685.1_SRR2107183_bin.57_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937873685.1_SRR2107183_bin.57_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 18:16:26,970] [INFO] Task succeeded: fastANI
[2023-06-29 18:16:27,001] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 18:16:27,002] [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_017305835.1	s__RCIO01 sp017305835	78.7674	426	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RCIO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004801285.1	s__Mesorhizobium composti	78.6371	417	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	96.99	96.99	0.90	0.90	2	-
GCA_003577315.1	s__Aquamicrobium_A sp003577315	78.6222	394	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904745.1	s__Oricola sp014904745	78.3935	434	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Oricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004963905.1	s__Mesorhizobium sp004963905	78.3017	408	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001014615.2	s__Aquamicrobium_A sp001014615	78.2867	402	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004791025.1	s__Mesorhizobium sp004791025	78.2498	475	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.99	98.05	0.93	0.88	18	-
GCF_001050155.1	s__Nitratireductor soli	78.2338	387	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952485.1	s__Mesorhizobium sp003952485	78.2278	439	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.38	98.21	0.91	0.89	5	-
GCA_004020545.1	s__Mesorhizobium sp004020545	78.2178	424	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.24	97.54	0.89	0.86	9	-
GCF_006442795.1	s__Mesorhizobium sp006442795	78.1985	412	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952505.1	s__Mesorhizobium sp003952505	78.1928	445	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.46	98.78	0.92	0.87	11	-
GCF_003289965.1	s__Mesorhizobium atlanticum	78.0763	443	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012842935.1	s__DUSC01 sp012842935	78.0739	382	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__DUSC01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006442965.1	s__Mesorhizobium sp006442965	78.0585	435	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003952465.1	s__Mesorhizobium sp003952465	78.0233	451	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.37	98.09	0.92	0.88	6	-
GCF_003952385.1	s__Mesorhizobium sp003952385	77.9479	461	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.01	97.50	0.89	0.87	7	-
GCF_018555685.1	s__Aminobacter anthyllidis	77.8396	394	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013358405.1	s__Oricola thermophila	77.8242	333	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Oricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000372965.1	s__Aminobacter sp000372965	77.8029	378	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003149475.2	s__Roseitalea stylonematis	77.7435	346	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Roseitalea	95.0	98.99	98.97	0.96	0.95	13	-
GCF_014200015.1	s__Aminobacter niigataensis	77.7125	406	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	98.01	98.00	0.90	0.90	3	-
GCF_014191375.1	s__Paramesorhizobium sp014191375	77.5758	330	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Paramesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017642895.1	s__Roseitalea sp017642895	77.3428	318	1227	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Roseitalea	95.0	99.99	99.99	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2023-06-29 18:16:27,004] [INFO] GTDB search result was written to GCA_937873685.1_SRR2107183_bin.57_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 18:16:27,004] [INFO] ===== GTDB Search completed =====
[2023-06-29 18:16:27,011] [INFO] DFAST_QC result json was written to GCA_937873685.1_SRR2107183_bin.57_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-29 18:16:27,011] [INFO] DFAST_QC completed!
[2023-06-29 18:16:27,011] [INFO] Total running time: 0h1m39s