[2023-06-05 02:43:10,205] [INFO] DFAST_QC pipeline started.
[2023-06-05 02:43:10,207] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 02:43:10,207] [INFO] DQC Reference Directory: /var/lib/cwl/stg08cc104c-10d9-4612-a181-147284c1796e/dqc_reference
[2023-06-05 02:43:11,626] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 02:43:11,627] [INFO] Task started: Prodigal
[2023-06-05 02:43:11,627] [INFO] Running command: gunzip -c /var/lib/cwl/stgdfceab2c-4375-4518-998f-7deeb50f3d58/GCA_902754485.1_SRR3727516_bin76_mag_fasta_genomic.fna.gz | prodigal -d GCA_902754485.1_SRR3727516_bin76_mag_fasta_genomic.fna/cds.fna -a GCA_902754485.1_SRR3727516_bin76_mag_fasta_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 02:43:15,551] [INFO] Task succeeded: Prodigal
[2023-06-05 02:43:15,551] [INFO] Task started: HMMsearch
[2023-06-05 02:43:15,552] [INFO] Running command: hmmsearch --tblout GCA_902754485.1_SRR3727516_bin76_mag_fasta_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg08cc104c-10d9-4612-a181-147284c1796e/dqc_reference/reference_markers.hmm GCA_902754485.1_SRR3727516_bin76_mag_fasta_genomic.fna/protein.faa > /dev/null
[2023-06-05 02:43:15,794] [INFO] Task succeeded: HMMsearch
[2023-06-05 02:43:15,795] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgdfceab2c-4375-4518-998f-7deeb50f3d58/GCA_902754485.1_SRR3727516_bin76_mag_fasta_genomic.fna.gz]
[2023-06-05 02:43:15,816] [INFO] Query marker FASTA was written to GCA_902754485.1_SRR3727516_bin76_mag_fasta_genomic.fna/markers.fasta
[2023-06-05 02:43:15,817] [INFO] Task started: Blastn
[2023-06-05 02:43:15,817] [INFO] Running command: blastn -query GCA_902754485.1_SRR3727516_bin76_mag_fasta_genomic.fna/markers.fasta -db /var/lib/cwl/stg08cc104c-10d9-4612-a181-147284c1796e/dqc_reference/reference_markers.fasta -out GCA_902754485.1_SRR3727516_bin76_mag_fasta_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:43:16,487] [INFO] Task succeeded: Blastn
[2023-06-05 02:43:16,493] [INFO] Selected 27 target genomes.
[2023-06-05 02:43:16,494] [INFO] Target genome list was writen to GCA_902754485.1_SRR3727516_bin76_mag_fasta_genomic.fna/target_genomes.txt
[2023-06-05 02:43:16,501] [INFO] Task started: fastANI
[2023-06-05 02:43:16,501] [INFO] Running command: fastANI --query /var/lib/cwl/stgdfceab2c-4375-4518-998f-7deeb50f3d58/GCA_902754485.1_SRR3727516_bin76_mag_fasta_genomic.fna.gz --refList GCA_902754485.1_SRR3727516_bin76_mag_fasta_genomic.fna/target_genomes.txt --output GCA_902754485.1_SRR3727516_bin76_mag_fasta_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 02:43:30,549] [INFO] Task succeeded: fastANI
[2023-06-05 02:43:30,550] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg08cc104c-10d9-4612-a181-147284c1796e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 02:43:30,551] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg08cc104c-10d9-4612-a181-147284c1796e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 02:43:30,565] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 02:43:30,566] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 02:43:30,566] [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
Idiomarina mangrovi	strain=ZQ330	GCA_003999375.1	2487133	2487133	type	True	81.2879	284	394	95	below_threshold
Pseudidiomarina salinarum	strain=ISL-52	GCA_003987105.1	435908	435908	type	True	78.5717	72	394	95	below_threshold
Pseudidiomarina piscicola	strain=CECT 9734	GCA_902806985.1	2614830	2614830	type	True	78.5508	64	394	95	below_threshold
Pseudidiomarina salinarum	strain=ISL-52	GCA_000753715.1	435908	435908	type	True	78.4868	72	394	95	below_threshold
Pseudidiomarina tainanensis	strain=PIN1	GCA_004214835.1	502365	502365	type	True	78.2124	91	394	95	below_threshold
Pseudidiomarina maritima	strain=CGMCC 1.7285	GCA_900115255.1	519453	519453	type	True	78.1528	90	394	95	below_threshold
Pseudidiomarina indica	strain=CGMCC 1.10824	GCA_900104245.1	1159017	1159017	type	True	78.1296	64	394	95	below_threshold
Pseudidiomarina donghaiensis	strain=908033	GCA_003987405.1	519452	519452	type	True	78.1077	101	394	95	below_threshold
Pseudidiomarina woesei	strain=DSM 27808	GCA_001517265.1	1381080	1381080	type	True	78.1074	91	394	95	below_threshold
Pseudidiomarina woesei	strain=DSM 27808	GCA_001418345.1	1381080	1381080	type	True	78.1074	91	394	95	below_threshold
Pseudidiomarina aestuarii	strain=KYW314	GCA_003987355.1	624146	624146	suspected-type	True	78.0206	77	394	95	below_threshold
Pseudidiomarina gelatinasegens	strain=R04H25	GCA_004025325.1	2487740	2487740	type	True	77.8794	80	394	95	below_threshold
Pseudidiomarina insulisalsae	strain=CVS-6	GCA_003987065.1	575789	575789	type	True	77.8649	77	394	95	below_threshold
Pseudidiomarina donghaiensis	strain=CGMCC 1.7284	GCA_900116895.1	519452	519452	type	True	77.8393	100	394	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 02:43:30,569] [INFO] DFAST Taxonomy check result was written to GCA_902754485.1_SRR3727516_bin76_mag_fasta_genomic.fna/tc_result.tsv
[2023-06-05 02:43:30,570] [INFO] ===== Taxonomy check completed =====
[2023-06-05 02:43:30,570] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 02:43:30,570] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg08cc104c-10d9-4612-a181-147284c1796e/dqc_reference/checkm_data
[2023-06-05 02:43:30,571] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 02:43:30,611] [INFO] Task started: CheckM
[2023-06-05 02:43:30,611] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902754485.1_SRR3727516_bin76_mag_fasta_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902754485.1_SRR3727516_bin76_mag_fasta_genomic.fna/checkm_input GCA_902754485.1_SRR3727516_bin76_mag_fasta_genomic.fna/checkm_result
[2023-06-05 02:43:49,891] [INFO] Task succeeded: CheckM
[2023-06-05 02:43:49,892] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.97%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-05 02:43:49,923] [INFO] ===== Completeness check finished =====
[2023-06-05 02:43:49,924] [INFO] ===== Start GTDB Search =====
[2023-06-05 02:43:49,924] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902754485.1_SRR3727516_bin76_mag_fasta_genomic.fna/markers.fasta)
[2023-06-05 02:43:49,924] [INFO] Task started: Blastn
[2023-06-05 02:43:49,925] [INFO] Running command: blastn -query GCA_902754485.1_SRR3727516_bin76_mag_fasta_genomic.fna/markers.fasta -db /var/lib/cwl/stg08cc104c-10d9-4612-a181-147284c1796e/dqc_reference/reference_markers_gtdb.fasta -out GCA_902754485.1_SRR3727516_bin76_mag_fasta_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:43:50,841] [INFO] Task succeeded: Blastn
[2023-06-05 02:43:50,845] [INFO] Selected 23 target genomes.
[2023-06-05 02:43:50,846] [INFO] Target genome list was writen to GCA_902754485.1_SRR3727516_bin76_mag_fasta_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 02:43:51,343] [INFO] Task started: fastANI
[2023-06-05 02:43:51,344] [INFO] Running command: fastANI --query /var/lib/cwl/stgdfceab2c-4375-4518-998f-7deeb50f3d58/GCA_902754485.1_SRR3727516_bin76_mag_fasta_genomic.fna.gz --refList GCA_902754485.1_SRR3727516_bin76_mag_fasta_genomic.fna/target_genomes_gtdb.txt --output GCA_902754485.1_SRR3727516_bin76_mag_fasta_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 02:44:01,669] [INFO] Task succeeded: fastANI
[2023-06-05 02:44:01,687] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 02:44:01,688] [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_003999375.1	s__Pseudidiomarina mangrovi	81.2793	285	394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002423905.1	s__Pseudidiomarina sp002423905	80.1657	229	394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009734345.1	s__Pseudidiomarina andamanensis	78.9417	84	394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902806985.1	s__Pseudidiomarina piscicola	78.5508	64	394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003987225.1	s__Pseudidiomarina homiensis	78.5071	76	394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000753715.1	s__Pseudidiomarina salinarum	78.4893	72	394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002279005.1	s__Pseudidiomarina sp002279005	78.3466	70	394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004214835.1	s__Pseudidiomarina tainanensis	78.255	90	394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	97.72	97.72	0.94	0.94	2	-
GCF_003182315.1	s__Pseudidiomarina maritima_A	78.1925	90	394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	98.70	97.84	0.93	0.89	6	-
GCF_900104245.1	s__Pseudidiomarina indica	78.152	63	394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418345.1	s__Pseudidiomarina woesei	78.1074	91	394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003987355.1	s__Pseudidiomarina aestuarii	78.0206	77	394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004025325.1	s__Pseudidiomarina gelatinasegens	77.9236	79	394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116895.1	s__Pseudidiomarina donghaiensis	77.8393	100	394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	0.99	0.99	2	-
GCA_018222985.1	s__Pseudidiomarina sp018222985	77.7996	90	394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000299895.1	s__Idiomarina xiamenensis	77.3596	55	394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 02:44:01,690] [INFO] GTDB search result was written to GCA_902754485.1_SRR3727516_bin76_mag_fasta_genomic.fna/result_gtdb.tsv
[2023-06-05 02:44:01,691] [INFO] ===== GTDB Search completed =====
[2023-06-05 02:44:01,695] [INFO] DFAST_QC result json was written to GCA_902754485.1_SRR3727516_bin76_mag_fasta_genomic.fna/dqc_result.json
[2023-06-05 02:44:01,695] [INFO] DFAST_QC completed!
[2023-06-05 02:44:01,695] [INFO] Total running time: 0h0m51s