[2024-01-24 11:43:51,961] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:51,963] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:51,963] [INFO] DQC Reference Directory: /var/lib/cwl/stgdf2dff15-15ae-4280-80a4-fa6cd67d17e5/dqc_reference
[2024-01-24 11:43:53,219] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:53,220] [INFO] Task started: Prodigal
[2024-01-24 11:43:53,220] [INFO] Running command: gunzip -c /var/lib/cwl/stg5b13f21c-df29-4b18-82c4-9f59f2d1c245/GCF_014218355.1_ASM1421835v1_genomic.fna.gz | prodigal -d GCF_014218355.1_ASM1421835v1_genomic.fna/cds.fna -a GCF_014218355.1_ASM1421835v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:04,310] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:04,310] [INFO] Task started: HMMsearch
[2024-01-24 11:44:04,310] [INFO] Running command: hmmsearch --tblout GCF_014218355.1_ASM1421835v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdf2dff15-15ae-4280-80a4-fa6cd67d17e5/dqc_reference/reference_markers.hmm GCF_014218355.1_ASM1421835v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:04,592] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:04,593] [INFO] Found 6/6 markers.
[2024-01-24 11:44:04,633] [INFO] Query marker FASTA was written to GCF_014218355.1_ASM1421835v1_genomic.fna/markers.fasta
[2024-01-24 11:44:04,634] [INFO] Task started: Blastn
[2024-01-24 11:44:04,634] [INFO] Running command: blastn -query GCF_014218355.1_ASM1421835v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf2dff15-15ae-4280-80a4-fa6cd67d17e5/dqc_reference/reference_markers.fasta -out GCF_014218355.1_ASM1421835v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:05,236] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:05,240] [INFO] Selected 15 target genomes.
[2024-01-24 11:44:05,241] [INFO] Target genome list was writen to GCF_014218355.1_ASM1421835v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:05,246] [INFO] Task started: fastANI
[2024-01-24 11:44:05,246] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b13f21c-df29-4b18-82c4-9f59f2d1c245/GCF_014218355.1_ASM1421835v1_genomic.fna.gz --refList GCF_014218355.1_ASM1421835v1_genomic.fna/target_genomes.txt --output GCF_014218355.1_ASM1421835v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:16,197] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:16,197] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdf2dff15-15ae-4280-80a4-fa6cd67d17e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:16,198] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdf2dff15-15ae-4280-80a4-fa6cd67d17e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:16,205] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:16,205] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:16,206] [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
Anaerocolumna chitinilytica	strain=CTTW	GCA_014218355.1	1727145	1727145	type	True	100.0	1873	1873	95	conclusive
Anaerocolumna jejuensis	strain=DSM 15929	GCA_900142215.1	259063	259063	type	True	80.2012	807	1873	95	below_threshold
Anaerocolumna xylanovorans	strain=DSM 12503	GCA_900143645.1	100134	100134	type	True	80.0365	750	1873	95	below_threshold
Anaerocolumna cellulosilytica	strain=SN021	GCA_014218335.1	433286	433286	type	True	78.0922	218	1873	95	below_threshold
Anaerocolumna aminovalerica	strain=DSM 1283	GCA_900115365.1	1527	1527	type	True	77.8605	132	1873	95	below_threshold
Anaerocolumna cellulosilytica	strain=DSM 100423	GCA_014202875.1	433286	433286	type	True	77.41	207	1873	95	below_threshold
Velocimicrobium porci	strain=WCA-693-APC-MOT-I	GCA_009696045.1	2606634	2606634	type	True	77.0117	60	1873	95	below_threshold
Anaerosporobacter faecicola	strain=KCTC 15857	GCA_012070565.1	2718714	2718714	type	True	76.699	68	1873	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:16,207] [INFO] DFAST Taxonomy check result was written to GCF_014218355.1_ASM1421835v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:16,208] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:16,208] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:16,208] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdf2dff15-15ae-4280-80a4-fa6cd67d17e5/dqc_reference/checkm_data
[2024-01-24 11:44:16,209] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:16,259] [INFO] Task started: CheckM
[2024-01-24 11:44:16,259] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014218355.1_ASM1421835v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014218355.1_ASM1421835v1_genomic.fna/checkm_input GCF_014218355.1_ASM1421835v1_genomic.fna/checkm_result
[2024-01-24 11:44:52,035] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:52,036] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:52,054] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:52,054] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:52,055] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014218355.1_ASM1421835v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:52,055] [INFO] Task started: Blastn
[2024-01-24 11:44:52,055] [INFO] Running command: blastn -query GCF_014218355.1_ASM1421835v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf2dff15-15ae-4280-80a4-fa6cd67d17e5/dqc_reference/reference_markers_gtdb.fasta -out GCF_014218355.1_ASM1421835v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:53,055] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:53,058] [INFO] Selected 15 target genomes.
[2024-01-24 11:44:53,058] [INFO] Target genome list was writen to GCF_014218355.1_ASM1421835v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:53,068] [INFO] Task started: fastANI
[2024-01-24 11:44:53,068] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b13f21c-df29-4b18-82c4-9f59f2d1c245/GCF_014218355.1_ASM1421835v1_genomic.fna.gz --refList GCF_014218355.1_ASM1421835v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014218355.1_ASM1421835v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:04,918] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:04,927] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:04,927] [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_014218355.1	s__Anaerocolumna sp014218355	100.0	1873	1873	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerocolumna	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900142215.1	s__Anaerocolumna jejuensis	80.2105	806	1873	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerocolumna	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900143645.1	s__Anaerocolumna xylanovorans	80.0549	746	1873	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerocolumna	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000702945.1	s__Anaerocolumna sp000702945	79.3411	492	1873	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerocolumna	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002434335.1	s__Anaerocolumna sp002434335	78.6977	449	1873	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerocolumna	95.0	99.22	99.22	0.91	0.91	2	-
GCF_014218335.1	s__Anaerocolumna cellulosilytica	78.0219	218	1873	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerocolumna	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900115365.1	s__Anaerocolumna aminovalerica	77.8846	131	1873	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerocolumna	95.0	99.17	99.14	0.90	0.89	3	-
GCA_002419585.1	s__Velocimicrobium sp002419585	77.2318	60	1873	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Velocimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012070565.1	s__Anaerosporobacter sp012070565	76.699	68	1873	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerosporobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015655565.1	s__Anaerocolumna sp015655565	76.2591	68	1873	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerocolumna	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:04,928] [INFO] GTDB search result was written to GCF_014218355.1_ASM1421835v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:04,929] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:04,932] [INFO] DFAST_QC result json was written to GCF_014218355.1_ASM1421835v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:04,932] [INFO] DFAST_QC completed!
[2024-01-24 11:45:04,933] [INFO] Total running time: 0h1m13s