[2024-01-24 11:35:11,644] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:11,645] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:11,646] [INFO] DQC Reference Directory: /var/lib/cwl/stg18c7ff73-b688-4a85-82db-a5c8c243a16b/dqc_reference
[2024-01-24 11:35:12,966] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:12,967] [INFO] Task started: Prodigal
[2024-01-24 11:35:12,967] [INFO] Running command: gunzip -c /var/lib/cwl/stg65d42281-e98e-4676-9f6b-92e8cdeee780/GCF_004005815.1_ASM400581v1_genomic.fna.gz | prodigal -d GCF_004005815.1_ASM400581v1_genomic.fna/cds.fna -a GCF_004005815.1_ASM400581v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:32,916] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:32,916] [INFO] Task started: HMMsearch
[2024-01-24 11:35:32,916] [INFO] Running command: hmmsearch --tblout GCF_004005815.1_ASM400581v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg18c7ff73-b688-4a85-82db-a5c8c243a16b/dqc_reference/reference_markers.hmm GCF_004005815.1_ASM400581v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:33,253] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:33,254] [INFO] Found 6/6 markers.
[2024-01-24 11:35:33,295] [INFO] Query marker FASTA was written to GCF_004005815.1_ASM400581v1_genomic.fna/markers.fasta
[2024-01-24 11:35:33,295] [INFO] Task started: Blastn
[2024-01-24 11:35:33,295] [INFO] Running command: blastn -query GCF_004005815.1_ASM400581v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg18c7ff73-b688-4a85-82db-a5c8c243a16b/dqc_reference/reference_markers.fasta -out GCF_004005815.1_ASM400581v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:33,918] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:33,923] [INFO] Selected 22 target genomes.
[2024-01-24 11:35:33,924] [INFO] Target genome list was writen to GCF_004005815.1_ASM400581v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:33,938] [INFO] Task started: fastANI
[2024-01-24 11:35:33,938] [INFO] Running command: fastANI --query /var/lib/cwl/stg65d42281-e98e-4676-9f6b-92e8cdeee780/GCF_004005815.1_ASM400581v1_genomic.fna.gz --refList GCF_004005815.1_ASM400581v1_genomic.fna/target_genomes.txt --output GCF_004005815.1_ASM400581v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:52,979] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:52,980] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg18c7ff73-b688-4a85-82db-a5c8c243a16b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:52,980] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg18c7ff73-b688-4a85-82db-a5c8c243a16b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:52,995] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:52,996] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:52,996] [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
Mucilaginibacter limnophilus	strain=YBJ-36	GCA_004005815.1	1932778	1932778	type	True	100.0	1524	1525	95	conclusive
Mucilaginibacter roseus	strain=LMG 28454	GCA_021215455.1	1528868	1528868	type	True	78.6682	399	1525	95	below_threshold
Mucilaginibacter hurinus	strain=ZR32	GCA_003324525.1	2201324	2201324	type	True	77.8866	332	1525	95	below_threshold
Mucilaginibacter achroorhodeus	strain=MJ1a	GCA_007846095.1	2599294	2599294	type	True	77.7545	238	1525	95	below_threshold
Mucilaginibacter pallidiroseus	strain=dk17	GCA_007846085.1	2599295	2599295	type	True	77.643	232	1525	95	below_threshold
Mucilaginibacter oryzae	strain=DSM 19975	GCA_003148845.1	468058	468058	type	True	77.6359	266	1525	95	below_threshold
Mucilaginibacter celer	strain=HYN0043	GCA_003576455.2	2305508	2305508	type	True	77.6221	288	1525	95	below_threshold
Mucilaginibacter gossypiicola	strain=Gh-48	GCA_900110105.1	551995	551995	type	True	77.5822	272	1525	95	below_threshold
Mucilaginibacter gossypii	strain=Gh-67	GCA_900100945.1	551996	551996	type	True	77.5302	267	1525	95	below_threshold
Mucilaginibacter auburnensis	strain=DSM 28175	GCA_002797815.1	1457233	1457233	type	True	77.5071	219	1525	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=PP-F2FG21	GCA_004378255.1	1812349	1812349	type	True	77.4508	238	1525	95	below_threshold
Mucilaginibacter terrigena	strain=17JY9-4	GCA_004168255.1	2492395	2492395	type	True	77.4459	279	1525	95	below_threshold
Mucilaginibacter pankratovii	strain=ZT4R22	GCA_014773265.1	2772110	2772110	type	True	77.4097	264	1525	95	below_threshold
Mucilaginibacter gilvus	strain=F01003	GCA_004054195.1	2305909	2305909	type	True	77.3571	241	1525	95	below_threshold
Mucilaginibacter lappiensis	strain=ATCC BAA-1855	GCA_900155965.1	354630	354630	type	True	77.2527	243	1525	95	below_threshold
Mucilaginibacter glaciei	strain=ZB1P21	GCA_014773245.1	2772109	2772109	type	True	77.2447	204	1525	95	below_threshold
Mucilaginibacter gotjawali	strain=SA3-7	GCA_002355435.1	1550579	1550579	type	True	77.2366	219	1525	95	below_threshold
Mucilaginibacter lappiensis	strain=ANJLi2	GCA_014200545.1	354630	354630	type	True	77.1889	245	1525	95	below_threshold
Mucilaginibacter gotjawali	strain=CECT 8628	GCA_014191635.1	1550579	1550579	type	True	77.1785	217	1525	95	below_threshold
Mucilaginibacter robiniae	strain=F39-2	GCA_012849215.1	2728022	2728022	type	True	77.1533	183	1525	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:52,998] [INFO] DFAST Taxonomy check result was written to GCF_004005815.1_ASM400581v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:52,999] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:52,999] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:52,999] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg18c7ff73-b688-4a85-82db-a5c8c243a16b/dqc_reference/checkm_data
[2024-01-24 11:35:53,000] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:53,044] [INFO] Task started: CheckM
[2024-01-24 11:35:53,044] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004005815.1_ASM400581v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004005815.1_ASM400581v1_genomic.fna/checkm_input GCF_004005815.1_ASM400581v1_genomic.fna/checkm_result
[2024-01-24 11:36:49,286] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:49,288] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:49,310] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:49,310] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:49,310] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004005815.1_ASM400581v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:49,311] [INFO] Task started: Blastn
[2024-01-24 11:36:49,311] [INFO] Running command: blastn -query GCF_004005815.1_ASM400581v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg18c7ff73-b688-4a85-82db-a5c8c243a16b/dqc_reference/reference_markers_gtdb.fasta -out GCF_004005815.1_ASM400581v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:50,119] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:50,124] [INFO] Selected 23 target genomes.
[2024-01-24 11:36:50,124] [INFO] Target genome list was writen to GCF_004005815.1_ASM400581v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:50,193] [INFO] Task started: fastANI
[2024-01-24 11:36:50,193] [INFO] Running command: fastANI --query /var/lib/cwl/stg65d42281-e98e-4676-9f6b-92e8cdeee780/GCF_004005815.1_ASM400581v1_genomic.fna.gz --refList GCF_004005815.1_ASM400581v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004005815.1_ASM400581v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:37:10,062] [INFO] Task succeeded: fastANI
[2024-01-24 11:37:10,084] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:37:10,084] [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_004005815.1	s__Mucilaginibacter limnophilus	100.0	1524	1525	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_015223065.1	s__Mucilaginibacter sp015223065	78.3948	459	1525	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003324525.1	s__Mucilaginibacter hurinus	77.8866	332	1525	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007846095.1	s__Mucilaginibacter sp007846095	77.7545	238	1525	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003576455.2	s__Mucilaginibacter celer	77.6329	287	1525	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002013915.1	s__Mucilaginibacter pedocola	77.6292	272	1525	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002288635.1	s__Mucilaginibacter sp002288635	77.597	244	1525	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110105.1	s__Mucilaginibacter gossypiicola	77.5822	272	1525	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002257585.1	s__Mucilaginibacter xinganensis	77.5638	207	1525	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003664165.1	s__Mucilaginibacter sp003664165	77.5619	260	1525	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100945.1	s__Mucilaginibacter gossypii	77.5297	267	1525	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	96.19	95.83	0.85	0.84	10	-
GCF_002797815.1	s__Mucilaginibacter auburnensis	77.5071	219	1525	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898335.1	s__Mucilaginibacter sp001898335	77.4835	243	1525	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.32	99.30	0.92	0.89	3	-
GCF_900103125.1	s__Mucilaginibacter sp900103125	77.4664	259	1525	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004168255.1	s__Mucilaginibacter terrigena	77.4459	279	1525	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014773265.1	s__Mucilaginibacter pankratovii	77.4097	264	1525	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002355435.1	s__Mucilaginibacter gotjawali	77.2482	218	1525	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014773245.1	s__Mucilaginibacter glaciei	77.2447	204	1525	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013288235.1	s__Mucilaginibacter sp013288235	77.2214	160	1525	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.30	99.08	0.67	0.66	3	-
GCF_013149275.1	s__Mucilaginibacter sp013149275	77.1932	256	1525	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903891475.1	s__Mucilaginibacter sp903891475	77.0072	118	1525	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.95	99.95	0.98	0.98	3	-
GCA_018267005.1	s__Mucilaginibacter sp018267005	76.8098	105	1525	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013286325.1	s__Mucilaginibacter sp013286325	76.5744	122	1525	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:37:10,086] [INFO] GTDB search result was written to GCF_004005815.1_ASM400581v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:37:10,087] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:37:10,091] [INFO] DFAST_QC result json was written to GCF_004005815.1_ASM400581v1_genomic.fna/dqc_result.json
[2024-01-24 11:37:10,091] [INFO] DFAST_QC completed!
[2024-01-24 11:37:10,092] [INFO] Total running time: 0h1m58s